inst/markdown/user_groups.markdown

In CRI-iAtlas/iatlas.modules2: iAatlas Modules2

To create your own sample groups to use in analyses, upload a comma-separated value file ( CSV file ) in the form shown in this example, but with commas separating the values. The CSV file must be a plain text file.

Sample Alternate Cancer Subtyping Gender Molecular Alteration Predicted Immunotherapy Outcome TCGA-01-0639 group_a male activating Non-responder TCGA-02-0007 group_a female repressing Responder ... ... ... ... ... TCGA-02-0011 group_b female NA Partial responder

Sample column

One column must be named Sample. This column will contain the identifiers for the samples to include.

TCGA

The Sample column needs to contain (12-digit) TCGA participant barcode IDs. (ie. 'TCGA-02-0011')

PCAWG

The sample column need to contain the donor ID. (ie. 'DO1328')

Other columns

Other columns (one or more) contain sample groupings that you can later select for analysis. For example in the above, the third column contains gender, and the values in that column can thus be used to compare immune response in cancer in women to that in men.

Rows

Rows can be supplied for any subset of TCGA or PCAWG samples. Rows will be filtered out if they have an NA value for the selected group. For example, if Molecular Alteration is selected, the bottom row will be removed.

Example files

Example1

Example2

CRI-iAtlas/iatlas.modules2 documentation built on Dec. 19, 2024, 8:14 p.m.