The responses to all the questions is fantastic. I really feel like I can ask anything which is so helpful!
Having someone in the chat helping those who are remote and the instructor is comforting
In general, coding is new to me (I work with data entry, so I do know the relevance), but I learned more details of how it a code is a language to the computer and will output information/answers.
Understanding how R/R Studio/Posit imports data, and runs from the console.
Be patient. It takes some time getting used to R coming from elsewhere.
That in R you can use the equal sign to assign variables instead of the arrow
Yup, this ultimately is a matter of style. If you’re coming to R from another language, I encourage you to continue to use the = sign. Just know that <- is pretty common among R users.
I feel like I don’t know what is unclear just yet as I am still very new to this concept.
I’m a very beginner, most stuff was unclear so I need time to practice.
My brain wants to know what every line of code is doing, otherwise I get hung up on trying to figure it out and can’t process what’s happening next. R feels like a very unintuitive language to me after using SAS for many years.
Still not super clear how Quarto works.
Great point, it’s hard to know what you need to know when you’ve encountered something brand new. Be patient and curious, and please reach out when you need help.
The layout of Posit Cloud was a little confusing. The more we used it, the more I understood it, but it would have helped to have a little bit more of a tour of what all the windows are from the beginning.
If you haven’t already, I have recorded a video here that is a guided tour of the RStudio interface:
https://www.youtube.com/watch?v=oFmjHxl28H0
When to type into the console (bottom left) vs the source .qmd files (top left)
In general, you want to save your work, so I usually write my code in code chunks in a .qmd (Quarto Markdown file).
By the end of today, you should be able to:
Data structures stores information about data types.
Vector is a ordered collection of a data type. Each element of a vector contains a data type, and all elements of a vector must be the same type, such as numeric, character, or logical.
So, you can have numeric vector, character vector, and logical vector.
We use c() - the combine function to declare a vector
What happens when you mix data types in a vector? One of the data types is coerced to the other data type.
[1] "chris" "1" "2" You can use operations and functions on vectors.
Multiplication has a new meaning when used on a numeric vector and numeric data type! This is called operator overloading.
A lot of operations/functions in R are vectorized - you can apply a function to a single value or a whole vector. This will become very important later on.
😮
How about numeric vector multiplied by numeric vector?
[1] 4 6 0How many elements are in this vector?
[1] 3We subset vectors using the bracket [ ] operation.
Inside the bracket is either a single numeric value or an a numerical indexing vector containing numerical values. They dictate which elements of the vector to return.
Alternatively, instead of using numerical indexing vectors, we can use a logical indexing vector.
The logical indexing vector must be the same length as the vector to be subsetted, with TRUE indicating an element to keep, and FALSE indicating an element to drop.
You can also declare a vector sequence using the : operator:
[1] 1 2 3 4 5We don’t know which elements to subset off the top of our head! If we know which elements are > 50, then we can give the elements for an explicit subset.
Use a comparison operator to create a logical indexing vector:
Can you guess what we do next?
Subset a vector implicitly, in 3 steps:
[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE< less than
<= less or equal than
> greater than
>= greater than or equal to
== equal to
!= not equal to
Subset staff to not have “chris” in it.
data.framesA data.frame is a table such that
This is the data structure that we will be working with for the rest of class.
data.frame PropertiesRows:
[1] 1864data.frameshead(metadata)
View(metadata)
data.framesThe column name is a character vector that corresponds to the columns of the data.frame.
[1] "ModelID" "PatientID" "CellLineName"
[4] "StrippedCellLineName" "Age" "SourceType"
[7] "SangerModelID" "RRID" "DepmapModelType"
[10] "AgeCategory" "GrowthPattern" "LegacyMolecularSubtype"
[13] "PrimaryOrMetastasis" "SampleCollectionSite" "Sex"
[16] "SourceDetail" "LegacySubSubtype" "CatalogNumber"
[19] "CCLEName" "COSMICID" "PublicComments"
[22] "WTSIMasterCellID" "EngineeredModel" "TreatmentStatus"
[25] "OnboardedMedia" "PlateCoating" "OncotreeCode"
[28] "OncotreeSubtype" "OncotreePrimaryDisease" "OncotreeLineage" data.frameThe dataframe$<column_name> operation selects for a column by its column name and returns the column as a vector:
[1] "Ovary/Fallopian Tube" "Myeloid"
[3] "Bowel" "Myeloid"
[5] "Myeloid" "Myeloid"
[7] "Bowel" "Skin"
[9] "Bowel" "Bladder/Urinary Tract"
[11] "Lung" "Ovary/Fallopian Tube"
[13] "Skin" "Lung"
[15] "Kidney" "Breast"
[17] "Bladder/Urinary Tract" "Breast"
[19] "Lymphoid" "Lung"
[21] "Pancreas" "Pancreas"
[23] "Lymphoid" "CNS/Brain"
[25] "Bladder/Urinary Tract" "CNS/Brain"
[27] "Breast" "Lung"
[29] "Lung" "Pancreas"
[31] "Lymphoid" "Lung"
[33] "Myeloid" "Lung"
[35] "CNS/Brain" "Soft Tissue"
[37] "Lymphoid" "Bone"
[39] "CNS/Brain" "Bone"
[41] "Pancreas" "Fibroblast"
[43] "Breast" "Myeloid"
[45] "Kidney" "Esophagus/Stomach"
[47] "Ovary/Fallopian Tube" "Kidney"
[49] "Lymphoid" "Soft Tissue"
[51] "Bone" "Lymphoid"
[53] "Soft Tissue" "CNS/Brain"
[55] "Lymphoid" "Lymphoid"
[57] "Thyroid" "Lymphoid"
[59] "Pancreas" "Lymphoid"
[61] "Lung" "Fibroblast"
[63] "Lung" "Myeloid"
[65] "Lung" "CNS/Brain"
[67] "Lymphoid" "Lymphoid"
[69] "Lymphoid" "Fibroblast"
[71] "Myeloid" "Lymphoid"
[73] "Myeloid" "CNS/Brain"
[75] "Myeloid" "Lymphoid"
[77] "Peripheral Nervous System" "Fibroblast"
[79] "Myeloid" "Myeloid"
[81] "Bone" "Fibroblast"
[83] "Myeloid" "Pancreas"
[85] "Pleura" "Bone"
[87] "Fibroblast" "Bowel"
[89] "Prostate" "Ovary/Fallopian Tube"
[91] "Pleura" "Pancreas"
[93] "Pancreas" "CNS/Brain"
[95] "Kidney" "Breast"
[97] "CNS/Brain" "Peripheral Nervous System"
[99] "Soft Tissue" "Lymphoid"
[101] "CNS/Brain" "Ovary/Fallopian Tube"
[103] "Lymphoid" "Lymphoid"
[105] "Lymphoid" "Pancreas"
[107] "Pancreas" "Lung"
[109] "Esophagus/Stomach" "Breast"
[111] "Myeloid" "Myeloid"
[113] "Pancreas" "Prostate"
[115] "Ovary/Fallopian Tube" "Breast"
[117] "Pancreas" "Fibroblast"
[119] "Peripheral Nervous System" "Lung"
[121] "Lymphoid" "Ovary/Fallopian Tube"
[123] "Lymphoid" "Fibroblast"
[125] "CNS/Brain" "Bladder/Urinary Tract"
[127] "CNS/Brain" "Lung"
[129] "Lymphoid" "Fibroblast"
[131] "Ovary/Fallopian Tube" "Soft Tissue"
[133] "Fibroblast" "Fibroblast"
[135] "Peripheral Nervous System" "CNS/Brain"
[137] "Pancreas" "Pancreas"
[139] "Lymphoid" "Biliary Tract"
[141] "Bladder/Urinary Tract" "Lung"
[143] "Esophagus/Stomach" "Soft Tissue"
[145] "Myeloid" "Breast"
[147] "Breast" "Peripheral Nervous System"
[149] "Lung" "Lymphoid"
[151] "CNS/Brain" "Pleura"
[153] "Fibroblast" "Pancreas"
[155] "Lymphoid" "Lymphoid"
[157] "Lymphoid" "Kidney"
[159] "CNS/Brain" "Lung"
[161] "Lymphoid" "Head and Neck"
[163] "Pancreas" "Fibroblast"
[165] "Myeloid" "Lymphoid"
[167] "Myeloid" "Soft Tissue"
[169] "Prostate" "Kidney"
[171] "CNS/Brain" "Uterus"
[173] "Thyroid" "Fibroblast"
[175] "Lung" "Prostate"
[177] "Pancreas" "Lung"
[179] "Fibroblast" "Head and Neck"
[181] "Ampulla of Vater" "Lymphoid"
[183] "Fibroblast" "Fibroblast"
[185] "Lung" "Lung"
[187] "Head and Neck" "Kidney"
[189] "Myeloid" "Thyroid"
[191] "Uterus" "Lymphoid"
[193] "Fibroblast" "Myeloid"
[195] "Breast" "Lymphoid"
[197] "Myeloid" "Fibroblast"
[199] "CNS/Brain" "Soft Tissue"
[201] "Bowel" "Peripheral Nervous System"
[203] "Lymphoid" "Pancreas"
[205] "Lymphoid" "Head and Neck"
[207] "CNS/Brain" "Biliary Tract"
[209] "Bone" "CNS/Brain"
[211] "Breast" "Pancreas"
[213] "Fibroblast" "CNS/Brain"
[215] "Esophagus/Stomach" "Liver"
[217] "Myeloid" "Skin"
[219] "Lymphoid" "Liver"
[221] "Pancreas" "Breast"
[223] "Fibroblast" "Esophagus/Stomach"
[225] "Lymphoid" "Peripheral Nervous System"
[227] "Head and Neck" "Fibroblast"
[229] "Fibroblast" "CNS/Brain"
[231] "CNS/Brain" "Lymphoid"
[233] "Kidney" "Pancreas"
[235] "Bowel" "Ovary/Fallopian Tube"
[237] "Head and Neck" "Esophagus/Stomach"
[239] "Fibroblast" "Myeloid"
[241] "Bladder/Urinary Tract" "Pancreas"
[243] "CNS/Brain" "Lymphoid"
[245] "Kidney" "Esophagus/Stomach"
[247] "Breast" "Bowel"
[249] "Kidney" "Lung"
[251] "Bowel" "Bowel"
[253] "Head and Neck" "Esophagus/Stomach"
[255] "Ovary/Fallopian Tube" "Lung"
[257] "Breast" "Peripheral Nervous System"
[259] "Peripheral Nervous System" "Lung"
[261] "Kidney" "Myeloid"
[263] "Lung" "Pancreas"
[265] "Pancreas" "Lymphoid"
[267] "Biliary Tract" "CNS/Brain"
[269] "Pancreas" "Lymphoid"
[271] "Kidney" "CNS/Brain"
[273] "Skin" "Fibroblast"
[275] "Breast" "Breast"
[277] "Ovary/Fallopian Tube" "Bone"
[279] "Ovary/Fallopian Tube" "Pancreas"
[281] "Lung" "CNS/Brain"
[283] "Fibroblast" "Lymphoid"
[285] "Bowel" "Lymphoid"
[287] "Breast" "CNS/Brain"
[289] "Lung" "Ovary/Fallopian Tube"
[291] "Lung" "Uterus"
[293] "Myeloid" "Myeloid"
[295] "Bowel" "Lung"
[297] "Lung" "Myeloid"
[299] "Kidney" "Myeloid"
[301] "Uterus" "Esophagus/Stomach"
[303] "Skin" "Esophagus/Stomach"
[305] "Fibroblast" "Pancreas"
[307] "Ovary/Fallopian Tube" "Lung"
[309] "Peripheral Nervous System" "Lung"
[311] "Peripheral Nervous System" "Kidney"
[313] "Lung" "Lymphoid"
[315] "Liver" "Kidney"
[317] "Esophagus/Stomach" "Pleura"
[319] "Pancreas" "Myeloid"
[321] "Skin" "CNS/Brain"
[323] "Ovary/Fallopian Tube" "Esophagus/Stomach"
[325] "Myeloid" "Lung"
[327] "CNS/Brain" "CNS/Brain"
[329] "Breast" "Pleura"
[331] "Pancreas" "Ovary/Fallopian Tube"
[333] "Lymphoid" "Pleura"
[335] "Myeloid" "Lung"
[337] "Lymphoid" "Lung"
[339] "Fibroblast" "Peripheral Nervous System"
[341] "Bowel" "Lung"
[343] "Esophagus/Stomach" "Peripheral Nervous System"
[345] "Lymphoid" "Pancreas"
[347] "Skin" "Breast"
[349] "Bowel" "Esophagus/Stomach"
[351] "Breast" "Esophagus/Stomach"
[353] "Pancreas" "Lung"
[355] "Esophagus/Stomach" "Lymphoid"
[357] "Lung" "Bone"
[359] "Bowel" "Liver"
[361] "Myeloid" "Lymphoid"
[363] "Bone" "Lymphoid"
[365] "Peripheral Nervous System" "Pleura"
[367] "CNS/Brain" "Myeloid"
[369] "CNS/Brain" "Lymphoid"
[371] "Lymphoid" "Myeloid"
[373] "Breast" "Kidney"
[375] "CNS/Brain" "Ampulla of Vater"
[377] "Lung" "Lung"
[379] "Lymphoid" "Bowel"
[381] "Lung" "Esophagus/Stomach"
[383] "Bladder/Urinary Tract" "Kidney"
[385] "Myeloid" "Myeloid"
[387] "Lymphoid" "CNS/Brain"
[389] "Lung" "Bone"
[391] "Lung" "Liver"
[393] "Lung" "Lung"
[395] "Bladder/Urinary Tract" "Uterus"
[397] "Lymphoid" "Lung"
[399] "Bowel" "Skin"
[401] "Lymphoid" "Bowel"
[403] "Skin" "Lymphoid"
[405] "Myeloid" "Uterus"
[407] "Esophagus/Stomach" "Ovary/Fallopian Tube"
[409] "Bone" "Kidney"
[411] "Bowel" "Fibroblast"
[413] "Lung" "Head and Neck"
[415] "Lung" "Pancreas"
[417] "Bone" "Lymphoid"
[419] "Liver" "Bowel"
[421] "Liver" "Skin"
[423] "Bone" "Skin"
[425] "Lymphoid" "Esophagus/Stomach"
[427] "Kidney" "Kidney"
[429] "Ovary/Fallopian Tube" "Lung"
[431] "Myeloid" "Kidney"
[433] "Lung" "Uterus"
[435] "Lymphoid" "CNS/Brain"
[437] "Lung" "Myeloid"
[439] "Lymphoid" "Skin"
[441] "Lung" "Ovary/Fallopian Tube"
[443] "Lung" "CNS/Brain"
[445] "Peripheral Nervous System" "Lung"
[447] "Lung" "Uterus"
[449] "Skin" "Lung"
[451] "Esophagus/Stomach" "Lymphoid"
[453] "Lung" "CNS/Brain"
[455] "Thyroid" "Kidney"
[457] "Skin" "Kidney"
[459] "Ovary/Fallopian Tube" "Biliary Tract"
[461] "Myeloid" "Lung"
[463] "CNS/Brain" "Skin"
[465] "Esophagus/Stomach" "Bowel"
[467] "Pancreas" "CNS/Brain"
[469] "Bowel" "Liver"
[471] "Head and Neck" "Bladder/Urinary Tract"
[473] "Liver" "Liver"
[475] "Skin" "Liver"
[477] "CNS/Brain" "Liver"
[479] "Lung" "Lung"
[481] "Liver" "Kidney"
[483] "Esophagus/Stomach" "Bladder/Urinary Tract"
[485] "Myeloid" "Esophagus/Stomach"
[487] "Bowel" "Cervix"
[489] "Bowel" "Lymphoid"
[491] "Liver" "Ovary/Fallopian Tube"
[493] "Kidney" "Lung"
[495] "Myeloid" "Bone"
[497] "Head and Neck" "Bowel"
[499] "Pancreas" "Head and Neck"
[501] "CNS/Brain" "Soft Tissue"
[503] "Lung" "Esophagus/Stomach"
[505] "Lung" "Lymphoid"
[507] "Lung" "Lung"
[509] "Lymphoid" "Kidney"
[511] "Lung" "Lung"
[513] "Bone" "Pancreas"
[515] "Head and Neck" "Lymphoid"
[517] "Ovary/Fallopian Tube" "Lung"
[519] "Bladder/Urinary Tract" "Lung"
[521] "Ovary/Fallopian Tube" "Lung"
[523] "Fibroblast" "Ovary/Fallopian Tube"
[525] "Lung" "Fibroblast"
[527] "Lung" "Fibroblast"
[529] "Bowel" "Kidney"
[531] "Lymphoid" "Pancreas"
[533] "Breast" "Liver"
[535] "Bowel" "Fibroblast"
[537] "Fibroblast" "Lymphoid"
[539] "Ovary/Fallopian Tube" "CNS/Brain"
[541] "Esophagus/Stomach" "Bladder/Urinary Tract"
[543] "Head and Neck" "Bladder/Urinary Tract"
[545] "Head and Neck" "Head and Neck"
[547] "Skin" "Myeloid"
[549] "Bowel" "Lung"
[551] "Breast" "Kidney"
[553] "Cervix" "Myeloid"
[555] "CNS/Brain" "Lung"
[557] "Esophagus/Stomach" "Esophagus/Stomach"
[559] "Lung" "Lung"
[561] "Lymphoid" "Bowel"
[563] "Bladder/Urinary Tract" "Lymphoid"
[565] "Breast" "Pleura"
[567] "CNS/Brain" "CNS/Brain"
[569] "Skin" "Breast"
[571] "Ovary/Fallopian Tube" "Lung"
[573] "Lymphoid" "Liver"
[575] "Lung" "Skin"
[577] "Skin" "Esophagus/Stomach"
[579] "Skin" "Lymphoid"
[581] "Ovary/Fallopian Tube" "Lung"
[583] "Lung" "Lung"
[585] "Lymphoid" "Lung"
[587] "Lung" "CNS/Brain"
[589] "CNS/Brain" "Bladder/Urinary Tract"
[591] "Lung" "CNS/Brain"
[593] "Lung" "CNS/Brain"
[595] "Lymphoid" "Pancreas"
[597] "Kidney" "Pancreas"
[599] "Myeloid" "Lung"
[601] "Myeloid" "Esophagus/Stomach"
[603] "Head and Neck" "Soft Tissue"
[605] "Ovary/Fallopian Tube" "CNS/Brain"
[607] "Lung" "Lymphoid"
[609] "Lymphoid" "Bone"
[611] "Skin" "Skin"
[613] "Esophagus/Stomach" "Ovary/Fallopian Tube"
[615] "Head and Neck" "Head and Neck"
[617] "Liver" "Breast"
[619] "CNS/Brain" "CNS/Brain"
[621] "Breast" "Liver"
[623] "Lymphoid" "Lung"
[625] "Lung" "CNS/Brain"
[627] "Head and Neck" "CNS/Brain"
[629] "Skin" "Esophagus/Stomach"
[631] "CNS/Brain" "Ovary/Fallopian Tube"
[633] "Lymphoid" "Esophagus/Stomach"
[635] "Lung" "Lung"
[637] "Skin" "Myeloid"
[639] "Breast" "Breast"
[641] "Skin" "Pleura"
[643] "Ovary/Fallopian Tube" "Esophagus/Stomach"
[645] "Pleura" "Kidney"
[647] "Skin" "Bowel"
[649] "Pancreas" "Lymphoid"
[651] "Lymphoid" "CNS/Brain"
[653] "Lymphoid" "Ovary/Fallopian Tube"
[655] "Lymphoid" "Lung"
[657] "Lymphoid" "Skin"
[659] "Lung" "Ovary/Fallopian Tube"
[661] "Lymphoid" "Lung"
[663] "Lung" "Lung"
[665] "Breast" "Lung"
[667] "Lung" "Liver"
[669] "Lung" "CNS/Brain"
[671] "Esophagus/Stomach" "Lung"
[673] "CNS/Brain" "Lung"
[675] "Esophagus/Stomach" "Esophagus/Stomach"
[677] "Bowel" "Lung"
[679] "Head and Neck" "Bowel"
[681] "Kidney" "Pancreas"
[683] "Liver" "Lymphoid"
[685] "Ovary/Fallopian Tube" "Soft Tissue"
[687] "Lung" "Breast"
[689] "Head and Neck" "Esophagus/Stomach"
[691] "Esophagus/Stomach" "Lung"
[693] "Ovary/Fallopian Tube" "Lymphoid"
[695] "Lung" "Breast"
[697] "Lung" "Ovary/Fallopian Tube"
[699] "Lymphoid" "Lung"
[701] "Ovary/Fallopian Tube" "Lung"
[703] "Lung" "Lymphoid"
[705] "Bowel" "Kidney"
[707] "Bowel" "Breast"
[709] "Lung" "Ovary/Fallopian Tube"
[711] "Lymphoid" "Head and Neck"
[713] "Thyroid" "Esophagus/Stomach"
[715] "Lung" "Ovary/Fallopian Tube"
[717] "Bladder/Urinary Tract" "Breast"
[719] "Bowel" "Head and Neck"
[721] "Bladder/Urinary Tract" "Breast"
[723] "Esophagus/Stomach" "Lung"
[725] "Lymphoid" "Lung"
[727] "Skin" "Lung"
[729] "Head and Neck" "Lung"
[731] "Liver" "Head and Neck"
[733] "Esophagus/Stomach" "Lung"
[735] "CNS/Brain" "Liver"
[737] "Head and Neck" "Bladder/Urinary Tract"
[739] "Fibroblast" "Lung"
[741] "Lung" "Lymphoid"
[743] "Esophagus/Stomach" "Lung"
[745] "Bone" "Lung"
[747] "Skin" "Myeloid"
[749] "Lung" "Bladder/Urinary Tract"
[751] "Lymphoid" "Breast"
[753] "CNS/Brain" "Lung"
[755] "Esophagus/Stomach" "Breast"
[757] "CNS/Brain" "Esophagus/Stomach"
[759] "Head and Neck" "Lymphoid"
[761] "Esophagus/Stomach" "Skin"
[763] "Lung" "Lung"
[765] "Breast" "Lung"
[767] "Myeloid" "Head and Neck"
[769] "Soft Tissue" "Lymphoid"
[771] "Lung" "Lung"
[773] "CNS/Brain" "Esophagus/Stomach"
[775] "Head and Neck" "Lung"
[777] "Lung" "Lung"
[779] "Lymphoid" "Breast"
[781] "Esophagus/Stomach" "Lung"
[783] "Lymphoid" "Lung"
[785] "Skin" "Lung"
[787] "Lung" "Lung"
[789] "Kidney" "Esophagus/Stomach"
[791] "Head and Neck" "Lymphoid"
[793] "Ovary/Fallopian Tube" "Fibroblast"
[795] "Bowel" "Skin"
[797] "Lung" "Skin"
[799] "Bladder/Urinary Tract" "Lung"
[801] "Peripheral Nervous System" "Skin"
[803] "Lymphoid" "CNS/Brain"
[805] "Biliary Tract" "Esophagus/Stomach"
[807] "Skin" "Ovary/Fallopian Tube"
[809] "Skin" "Lung"
[811] "Skin" "Lymphoid"
[813] "Lung" "Lymphoid"
[815] "Breast" "CNS/Brain"
[817] "Bowel" "Lymphoid"
[819] "Skin" "Esophagus/Stomach"
[821] "Esophagus/Stomach" "Lung"
[823] "Lung" "Skin"
[825] "Breast" "Lymphoid"
[827] "Lung" "Uterus"
[829] "Head and Neck" "Soft Tissue"
[831] "Bladder/Urinary Tract" "Soft Tissue"
[833] "Head and Neck" "Lung"
[835] "Lymphoid" "Bladder/Urinary Tract"
[837] "Lung" "Lung"
[839] "Bowel" "Lung"
[841] "Lung" "Lung"
[843] "Head and Neck" "Esophagus/Stomach"
[845] "Liver" "Breast"
[847] "Fibroblast" "Lung"
[849] "Lung" "Lung"
[851] "Lymphoid" "Esophagus/Stomach"
[853] "Breast" "Breast"
[855] "Lung" "Breast"
[857] "Lung" "Lung"
[859] "Bladder/Urinary Tract" "CNS/Brain"
[861] "Uterus" "Esophagus/Stomach"
[863] "Lung" "Lung"
[865] "Lung" "Lung"
[867] "Lung" "Lung"
[869] "Lung" "Esophagus/Stomach"
[871] "Lymphoid" "Lung"
[873] "Breast" "Lymphoid"
[875] "Lung" "Uterus"
[877] "Esophagus/Stomach" "Skin"
[879] "Skin" "CNS/Brain"
[881] "Skin" "Ovary/Fallopian Tube"
[883] "Lung" "CNS/Brain"
[885] "Lung" "Lymphoid"
[887] "Lung" "Lung"
[889] "Lung" "Lung"
[891] "Lung" "Bowel"
[893] "Bladder/Urinary Tract" "Thyroid"
[895] "Esophagus/Stomach" "Skin"
[897] "Lung" "Lung"
[899] "Breast" "Thyroid"
[901] "Lung" "Bladder/Urinary Tract"
[903] "Ovary/Fallopian Tube" "Kidney"
[905] "Esophagus/Stomach" "Uterus"
[907] "Breast" "Esophagus/Stomach"
[909] "Lung" "Uterus"
[911] "Lymphoid" "Skin"
[913] "Lung" "Esophagus/Stomach"
[915] "Lymphoid" "Esophagus/Stomach"
[917] "Myeloid" "Lung"
[919] "Lymphoid" "Lymphoid"
[921] "Lung" "Lung"
[923] "Bowel" "Breast"
[925] "Uterus" "Lung"
[927] "Breast" "Skin"
[929] "Esophagus/Stomach" "Pancreas"
[931] "Breast" "Bowel"
[933] "Ovary/Fallopian Tube" "Lymphoid"
[935] "Lymphoid" "Uterus"
[937] "Uterus" "Uterus"
[939] "Lymphoid" "Bowel"
[941] "Lymphoid" "Lung"
[943] "Uterus" "Ovary/Fallopian Tube"
[945] "Esophagus/Stomach" "Esophagus/Stomach"
[947] "Bowel" "Lung"
[949] "Prostate" "Lymphoid"
[951] "Uterus" "Bowel"
[953] "Prostate" "Bowel"
[955] "Bowel" "Bowel"
[957] "Lymphoid" "Uterus"
[959] "Ovary/Fallopian Tube" "Bowel"
[961] "Lymphoid" "Uterus"
[963] "Ovary/Fallopian Tube" "Bowel"
[965] "Skin" "Bowel"
[967] "Bowel" "Bowel"
[969] "Uterus" "Bladder/Urinary Tract"
[971] "Uterus" "Lung"
[973] "Biliary Tract" "Prostate"
[975] "Uterus" "Prostate"
[977] "Lung" "Lymphoid"
[979] "Bowel" "Myeloid"
[981] "Uterus" "Bowel"
[983] "Bowel" "Skin"
[985] "Uterus" "Bowel"
[987] "Uterus" "Bowel"
[989] "Head and Neck" "Uterus"
[991] "Uterus" "Lymphoid"
[993] "Uterus" "Bowel"
[995] "Bowel" "Bowel"
[997] "CNS/Brain" "Bone"
[999] "Skin" "Bone"
[1001] "Bone" "Bone"
[1003] "Bone" "Bowel"
[1005] "CNS/Brain" "Cervix"
[1007] "Fibroblast" "CNS/Brain"
[1009] "Liver" "Bone"
[1011] "Head and Neck" "Skin"
[1013] "CNS/Brain" "Bone"
[1015] "Bone" "CNS/Brain"
[1017] "Bone" "CNS/Brain"
[1019] "Bone" "Bone"
[1021] "Myeloid" "Myeloid"
[1023] "Bone" "Bowel"
[1025] "Skin" "Uterus"
[1027] "Lymphoid" "Skin"
[1029] "Skin" "Lung"
[1031] "Ovary/Fallopian Tube" "Lung"
[1033] "Soft Tissue" "CNS/Brain"
[1035] "CNS/Brain" "CNS/Brain"
[1037] "CNS/Brain" "Lymphoid"
[1039] "CNS/Brain" "Lymphoid"
[1041] "Bowel" "Ovary/Fallopian Tube"
[1043] "Lymphoid" "Breast"
[1045] "Bone" "CNS/Brain"
[1047] "Lymphoid" "Cervix"
[1049] "Pancreas" "Lung"
[1051] "Lung" "Bowel"
[1053] "Bowel" "Cervix"
[1055] "Kidney" "Lung"
[1057] "Liver" "Head and Neck"
[1059] "Bowel" "Fibroblast"
[1061] "Bone" "Soft Tissue"
[1063] "Lymphoid" "Pancreas"
[1065] "CNS/Brain" "Lymphoid"
[1067] "Pancreas" "Lymphoid"
[1069] "Pancreas" "Kidney"
[1071] "Lymphoid" "Lung"
[1073] "CNS/Brain" "Lymphoid"
[1075] "Lymphoid" "Skin"
[1077] "Skin" "CNS/Brain"
[1079] "CNS/Brain" "Lymphoid"
[1081] "CNS/Brain" "Myeloid"
[1083] "Lymphoid" "Skin"
[1085] "Lymphoid" "Lymphoid"
[1087] "Lung" "Lung"
[1089] "Lung" "CNS/Brain"
[1091] "Lymphoid" "Ovary/Fallopian Tube"
[1093] "Ovary/Fallopian Tube" "Lymphoid"
[1095] "Lymphoid" "Lymphoid"
[1097] "Bone" "Ovary/Fallopian Tube"
[1099] "Lymphoid" "Kidney"
[1101] "Soft Tissue" "Skin"
[1103] "Pancreas" "CNS/Brain"
[1105] "Kidney" "Lymphoid"
[1107] "Bladder/Urinary Tract" "Soft Tissue"
[1109] "Peripheral Nervous System" "Soft Tissue"
[1111] "Skin" "Bone"
[1113] "Bone" "Kidney"
[1115] "Soft Tissue" "Lymphoid"
[1117] "CNS/Brain" "Bowel"
[1119] "Kidney" "CNS/Brain"
[1121] "Lymphoid" "Bone"
[1123] "Bone" "Fibroblast"
[1125] "Kidney" "Kidney"
[1127] "CNS/Brain" "CNS/Brain"
[1129] "CNS/Brain" "Kidney"
[1131] "Kidney" "Head and Neck"
[1133] "Head and Neck" "Head and Neck"
[1135] "Myeloid" "CNS/Brain"
[1137] "Lung" "Lung"
[1139] "Skin" "Breast"
[1141] "Soft Tissue" "Soft Tissue"
[1143] "Soft Tissue" "Soft Tissue"
[1145] "Soft Tissue" "Ovary/Fallopian Tube"
[1147] "Ovary/Fallopian Tube" "Soft Tissue"
[1149] "Bone" "Bone"
[1151] "CNS/Brain" "Eye"
[1153] "Peripheral Nervous System" "Peripheral Nervous System"
[1155] "Peripheral Nervous System" "Peripheral Nervous System"
[1157] "Thyroid" "Thyroid"
[1159] "Kidney" "Liver"
[1161] "Thyroid" "Soft Tissue"
[1163] "Skin" "CNS/Brain"
[1165] "Head and Neck" "Head and Neck"
[1167] "Cervix" "Cervix"
[1169] "Cervix" "Cervix"
[1171] "Peripheral Nervous System" "Skin"
[1173] "Ovary/Fallopian Tube" "Cervix"
[1175] "Peripheral Nervous System" "Bowel"
[1177] "Head and Neck" "Head and Neck"
[1179] "Thyroid" "Pancreas"
[1181] "Peripheral Nervous System" "Peripheral Nervous System"
[1183] "Thyroid" "Breast"
[1185] "Breast" "Cervix"
[1187] "Cervix" "Lung"
[1189] "Lung" "Lung"
[1191] "Lung" "Peripheral Nervous System"
[1193] "Peripheral Nervous System" "Esophagus/Stomach"
[1195] "Ovary/Fallopian Tube" "Ovary/Fallopian Tube"
[1197] "Ovary/Fallopian Tube" "Ovary/Fallopian Tube"
[1199] "Pancreas" "Pancreas"
[1201] "Pancreas" "Pancreas"
[1203] "Pancreas" "Pancreas"
[1205] "Pancreas" "Prostate"
[1207] "Thyroid" "Head and Neck"
[1209] "Lung" "Breast"
[1211] "Breast" "Breast"
[1213] "Breast" "Breast"
[1215] "Breast" "Breast"
[1217] "Breast" "Breast"
[1219] "Breast" "Kidney"
[1221] "Bowel" "Vulva/Vagina"
[1223] "Adrenal Gland" "Cervix"
[1225] "Ovary/Fallopian Tube" "Bladder/Urinary Tract"
[1227] "Bladder/Urinary Tract" "Bladder/Urinary Tract"
[1229] "Bladder/Urinary Tract" "Bladder/Urinary Tract"
[1231] "Bladder/Urinary Tract" "Bladder/Urinary Tract"
[1233] "Bladder/Urinary Tract" "Bladder/Urinary Tract"
[1235] "Bladder/Urinary Tract" "Lung"
[1237] "Ovary/Fallopian Tube" "Breast"
[1239] "Eye" "Prostate"
[1241] "Bone" "Bone"
[1243] "Soft Tissue" "Eye"
[1245] "Skin" "Thyroid"
[1247] "Lymphoid" "Cervix"
[1249] "Lymphoid" "Prostate"
[1251] "Bowel" "Bowel"
[1253] "Bowel" "Bowel"
[1255] "Bowel" "Bowel"
[1257] "Peripheral Nervous System" "Lymphoid"
[1259] "Lymphoid" "Lung"
[1261] "Lung" "Biliary Tract"
[1263] "Uterus" "Esophagus/Stomach"
[1265] "Esophagus/Stomach" "Lymphoid"
[1267] "Esophagus/Stomach" "Head and Neck"
[1269] "Head and Neck" "Head and Neck"
[1271] "Cervix" "Breast"
[1273] "Cervix" "Cervix"
[1275] "Uterus" "Uterus"
[1277] "Bone" "Lymphoid"
[1279] "Skin" "Skin"
[1281] "Skin" "Skin"
[1283] "Cervix" "Bone"
[1285] "Thyroid" "Uterus"
[1287] "Uterus" "Kidney"
[1289] "Lymphoid" "Biliary Tract"
[1291] "Biliary Tract" "Lymphoid"
[1293] "Soft Tissue" "Lymphoid"
[1295] "Head and Neck" "Head and Neck"
[1297] "Esophagus/Stomach" "Pleura"
[1299] "Peripheral Nervous System" "Lung"
[1301] "Skin" "Skin"
[1303] "Skin" "Eye"
[1305] "Pleura" "Pleura"
[1307] "Pleura" "Pleura"
[1309] "Pleura" "Pleura"
[1311] "Pleura" "Pleura"
[1313] "Skin" "Skin"
[1315] "Skin" "Skin"
[1317] "Skin" "Skin"
[1319] "Myeloid" "Myeloid"
[1321] "Myeloid" "Testis"
[1323] "Lung" "Lung"
[1325] "Peripheral Nervous System" "CNS/Brain"
[1327] "CNS/Brain" "Biliary Tract"
[1329] "CNS/Brain" "CNS/Brain"
[1331] "CNS/Brain" "CNS/Brain"
[1333] "Myeloid" "Lymphoid"
[1335] "Lymphoid" "Myeloid"
[1337] "Biliary Tract" "CNS/Brain"
[1339] "CNS/Brain" "CNS/Brain"
[1341] "Head and Neck" "Head and Neck"
[1343] "Prostate" "Ovary/Fallopian Tube"
[1345] "Ovary/Fallopian Tube" "Ovary/Fallopian Tube"
[1347] "Lymphoid" "Lymphoid"
[1349] "Lymphoid" "Lymphoid"
[1351] "Head and Neck" "Lymphoid"
[1353] "Skin" "Myeloid"
[1355] "Prostate" "Prostate"
[1357] "Cervix" "Cervix"
[1359] "Cervix" "Esophagus/Stomach"
[1361] "Esophagus/Stomach" "Uterus"
[1363] "Myeloid" "Esophagus/Stomach"
[1365] "Testis" "Lymphoid"
[1367] "CNS/Brain" "Biliary Tract"
[1369] "Peripheral Nervous System" "Head and Neck"
[1371] "Lymphoid" "Lymphoid"
[1373] "Lymphoid" "Kidney"
[1375] "Kidney" "Head and Neck"
[1377] "Head and Neck" "Head and Neck"
[1379] "Head and Neck" "Head and Neck"
[1381] "Head and Neck" "Head and Neck"
[1383] "Head and Neck" "Soft Tissue"
[1385] "Lymphoid" "Skin"
[1387] "Lymphoid" "Lymphoid"
[1389] "CNS/Brain" "Bone"
[1391] "Bone" "Peripheral Nervous System"
[1393] "Ovary/Fallopian Tube" "Lymphoid"
[1395] "Lymphoid" "Lymphoid"
[1397] "Lymphoid" "Soft Tissue"
[1399] "Soft Tissue" "Soft Tissue"
[1401] "Soft Tissue" "Soft Tissue"
[1403] "Soft Tissue" "Fibroblast"
[1405] "Bowel" "Soft Tissue"
[1407] "Soft Tissue" "Soft Tissue"
[1409] "Soft Tissue" "Soft Tissue"
[1411] "Soft Tissue" "Soft Tissue"
[1413] "Soft Tissue" "Soft Tissue"
[1415] "Bone" "Bone"
[1417] "Breast" "Breast"
[1419] "Bowel" "Breast"
[1421] "Biliary Tract" "Biliary Tract"
[1423] "Biliary Tract" "Biliary Tract"
[1425] "Biliary Tract" "Biliary Tract"
[1427] "Biliary Tract" "Biliary Tract"
[1429] "Biliary Tract" "Biliary Tract"
[1431] "Biliary Tract" "Biliary Tract"
[1433] "Biliary Tract" "Biliary Tract"
[1435] "Biliary Tract" "Liver"
[1437] "Biliary Tract" "Biliary Tract"
[1439] "Biliary Tract" "Biliary Tract"
[1441] "Ampulla of Vater" "Biliary Tract"
[1443] "Biliary Tract" "Lung"
[1445] "Biliary Tract" "Biliary Tract"
[1447] "Biliary Tract" "Skin"
[1449] "Skin" "Pleura"
[1451] "Skin" "Skin"
[1453] "Skin" "Ovary/Fallopian Tube"
[1455] "Pleura" "Lymphoid"
[1457] "Biliary Tract" "Pancreas"
[1459] "Skin" "Skin"
[1461] "Skin" "Skin"
[1463] "Skin" "Eye"
[1465] "Eye" "Eye"
[1467] "Eye" "Eye"
[1469] "Eye" "Cervix"
[1471] "Cervix" "Uterus"
[1473] "Ampulla of Vater" "Bowel"
[1475] "Bowel" "Uterus"
[1477] "Uterus" "Head and Neck"
[1479] "Lung" "Ovary/Fallopian Tube"
[1481] "Pancreas" "Vulva/Vagina"
[1483] "Thyroid" "Head and Neck"
[1485] "Head and Neck" "Head and Neck"
[1487] "Head and Neck" "Uterus"
[1489] "Soft Tissue" "Lung"
[1491] "Lung" "Lymphoid"
[1493] "Lymphoid" "Lymphoid"
[1495] "Myeloid" "Lymphoid"
[1497] "Peripheral Nervous System" "Peripheral Nervous System"
[1499] "Bone" "Bone"
[1501] "CNS/Brain" "Lung"
[1503] "Peripheral Nervous System" "Peripheral Nervous System"
[1505] "Skin" "Soft Tissue"
[1507] "Lung" "Kidney"
[1509] "Vulva/Vagina" "Bone"
[1511] "Bone" "Bone"
[1513] "Lung" "Skin"
[1515] "Skin" "Skin"
[1517] "Bone" "Skin"
[1519] "Lung" "Lung"
[1521] "Bone" "Bone"
[1523] "Bone" "Bone"
[1525] "Bone" "Bone"
[1527] "Bone" "Bone"
[1529] "Bone" "Bone"
[1531] "Bone" "Bone"
[1533] "Bone" "Bone"
[1535] "Bone" "Bone"
[1537] "Bone" "Vulva/Vagina"
[1539] "Skin" "Lung"
[1541] "Pleura" "Pleura"
[1543] "Pleura" "Pleura"
[1545] "Pleura" "Pleura"
[1547] "Pleura" "Pleura"
[1549] "Pleura" "Pleura"
[1551] "Pleura" "Pleura"
[1553] "Pleura" "Pleura"
[1555] "Lung" "Kidney"
[1557] "Ovary/Fallopian Tube" "Esophagus/Stomach"
[1559] "Bone" "Skin"
[1561] "Lung" "Lung"
[1563] "Ovary/Fallopian Tube" "Skin"
[1565] "Thyroid" "Ovary/Fallopian Tube"
[1567] "Kidney" "Kidney"
[1569] "Skin" "Skin"
[1571] "Lung" "Kidney"
[1573] "Lung" "Lung"
[1575] "Lung" "Skin"
[1577] "Bone" "Esophagus/Stomach"
[1579] "Skin" "Breast"
[1581] "Pancreas" "Skin"
[1583] "Skin" "Kidney"
[1585] "Kidney" "Lung"
[1587] "Lung" "Lung"
[1589] "Lung" "Lung"
[1591] "Lung" "Lung"
[1593] "Lung" "Bone"
[1595] "Breast" "Cervix"
[1597] "Ovary/Fallopian Tube" "Ovary/Fallopian Tube"
[1599] "Ovary/Fallopian Tube" "Lung"
[1601] "Pancreas" "Pancreas"
[1603] "Kidney" "Kidney"
[1605] "Kidney" "Kidney"
[1607] "Kidney" "Kidney"
[1609] "Lung" "Kidney"
[1611] "Lung" "Lung"
[1613] "Other" "Kidney"
[1615] "Vulva/Vagina" "Cervix"
[1617] "Esophagus/Stomach" "Bone"
[1619] "Skin" "Skin"
[1621] "Skin" "Breast"
[1623] "Lymphoid" "Myeloid"
[1625] "Lymphoid" "Head and Neck"
[1627] "Head and Neck" "Lymphoid"
[1629] "Lymphoid" "Lymphoid"
[1631] "Peripheral Nervous System" "Myeloid"
[1633] "Bowel" "Lymphoid"
[1635] "Lymphoid" "Lymphoid"
[1637] "CNS/Brain" "CNS/Brain"
[1639] "CNS/Brain" "CNS/Brain"
[1641] "CNS/Brain" "CNS/Brain"
[1643] "CNS/Brain" "CNS/Brain"
[1645] "CNS/Brain" "Lymphoid"
[1647] "Bowel" "Head and Neck"
[1649] "Bladder/Urinary Tract" "Lymphoid"
[1651] "Biliary Tract" "Lymphoid"
[1653] "Head and Neck" "Lymphoid"
[1655] "Lymphoid" "Lymphoid"
[1657] "Esophagus/Stomach" "Head and Neck"
[1659] "Lymphoid" "Soft Tissue"
[1661] "Myeloid" "Peripheral Nervous System"
[1663] "Head and Neck" "Head and Neck"
[1665] "Head and Neck" "Lymphoid"
[1667] "Lymphoid" "Lymphoid"
[1669] "Lymphoid" "Lymphoid"
[1671] "CNS/Brain" "Myeloid"
[1673] "CNS/Brain" "Peripheral Nervous System"
[1675] "Myeloid" "Esophagus/Stomach"
[1677] "Esophagus/Stomach" "Head and Neck"
[1679] "Bladder/Urinary Tract" "Lymphoid"
[1681] "CNS/Brain" "CNS/Brain"
[1683] "Myeloid" "Soft Tissue"
[1685] "Lymphoid" "Myeloid"
[1687] "Lymphoid" "Lymphoid"
[1689] "Myeloid" "Peripheral Nervous System"
[1691] "Peripheral Nervous System" "Peripheral Nervous System"
[1693] "Peripheral Nervous System" "Peripheral Nervous System"
[1695] "Peripheral Nervous System" "Peripheral Nervous System"
[1697] "Peripheral Nervous System" "Peripheral Nervous System"
[1699] "Lung" "Bowel"
[1701] "Testis" "Lymphoid"
[1703] "Myeloid" "Testis"
[1705] "Esophagus/Stomach" "Lymphoid"
[1707] "Head and Neck" "Head and Neck"
[1709] "Head and Neck" "Head and Neck"
[1711] "Head and Neck" "Myeloid"
[1713] "Lymphoid" "Lymphoid"
[1715] "Myeloid" "CNS/Brain"
[1717] "Head and Neck" "Esophagus/Stomach"
[1719] "Lymphoid" "Lymphoid"
[1721] "Soft Tissue" "Soft Tissue"
[1723] "Esophagus/Stomach" "Biliary Tract"
[1725] "Lymphoid" "Myeloid"
[1727] "Myeloid" "Lymphoid"
[1729] "Breast" "Breast"
[1731] "Breast" "Breast"
[1733] "Breast" "Breast"
[1735] "Breast" "Breast"
[1737] "Breast" "Breast"
[1739] "Breast" "Breast"
[1741] "Breast" "Soft Tissue"
[1743] "Lung" "Soft Tissue"
[1745] "Eye" "Lung"
[1747] "Skin" "Lymphoid"
[1749] "Peripheral Nervous System" "Normal"
[1751] "Normal" "Normal"
[1753] "Bowel" "Normal"
[1755] "Normal" "CNS/Brain"
[1757] "CNS/Brain" "Normal"
[1759] "Normal" "Normal"
[1761] "Normal" "Normal"
[1763] "Normal" "Normal"
[1765] "Normal" "Normal"
[1767] "Normal" "Normal"
[1769] "Normal" "Normal"
[1771] "Normal" "Normal"
[1773] "Normal" "Normal"
[1775] "Normal" "Normal"
[1777] "Normal" "Normal"
[1779] "Normal" "Normal"
[1781] "Normal" "Normal"
[1783] "Normal" "Normal"
[1785] "Normal" "Normal"
[1787] "Normal" "Normal"
[1789] "Normal" "Normal"
[1791] "Normal" "Skin"
[1793] "Skin" "Skin"
[1795] "Peripheral Nervous System" "Lymphoid"
[1797] "Thyroid" "Breast"
[1799] "Esophagus/Stomach" "Skin"
[1801] "Skin" "Skin"
[1803] "Skin" "Eye"
[1805] "Eye" "Eye"
[1807] "Eye" "Eye"
[1809] "Eye" "Bone"
[1811] "Myeloid" "Lymphoid"
[1813] "Ovary/Fallopian Tube" "Skin"
[1815] "Skin" "Skin"
[1817] "Skin" "Skin"
[1819] "Liver" "Lung"
[1821] "Lung" "Biliary Tract"
[1823] "Lung" "Bowel"
[1825] "Bowel" "Bowel"
[1827] "Bowel" "Pancreas"
[1829] "CNS/Brain" "Eye"
[1831] "Peripheral Nervous System" "Peripheral Nervous System"
[1833] "Esophagus/Stomach" "Esophagus/Stomach"
[1835] "Esophagus/Stomach" "Pancreas"
[1837] "Pancreas" "Pancreas"
[1839] "Pancreas" "Pancreas"
[1841] "Esophagus/Stomach" "Soft Tissue"
[1843] "Peripheral Nervous System" "Peripheral Nervous System"
[1845] "Bone" "Esophagus/Stomach"
[1847] "Esophagus/Stomach" "Bowel"
[1849] "Skin" "Esophagus/Stomach"
[1851] "Breast" "Breast"
[1853] "Breast" "Peripheral Nervous System"
[1855] "Eye" "Breast"
[1857] "Breast" "Esophagus/Stomach"
[1859] "Esophagus/Stomach" "Esophagus/Stomach"
[1861] "Esophagus/Stomach" "Esophagus/Stomach"
[1863] "Esophagus/Stomach" "Lung" data.frame[1] 60 36 72 30 30Challenge!
[1] 36 30 30 64 35 10 77 55 38 35 NA 66 29 63 65 1 64 31 29 71 33 24 58 7 23
[26] 5 47 29 44 73 57 20 77 76 59 35 37 45 40 3 68 46 53 13 0 22 0 62 7 36
[51] 32 0 0 64 64 41 20 63 35 56 37 22 53 33 NA NA 2 28 81 26 52 33 69 51 37
[76] 5 40data.framedataframe[row_idx, col_idx] subsets the data.frame by a row indexing vector row_idx, and a column indexing vector col_idx.
data.framesWe can refer to the column names directly:
data.frameWe can leave the column index or row index empty to just subset columns or rows.