Krabmen

Download data

• To download the necessery TCGA data please run scripts/r/download-tcga-mrna.R.

• This script downloads TCGA data into the download directory.

• To extract headers from the file (for barcode analysis) please run scripts/first-line.sh. These headers can be used to generate barcode stats.

• Next run scripts/r/count.R to generate statistics of all barcodes in results/stats. These statistics are a summary of barcodes of the TCGA data - how many tumor vs how many normal cells are in each tumor file. The file count.R has a variable headers.dir which should be set to either the normalized or raw data header directory.

Expression level

Run negative binomial test, H0 = mean expression level for tumor and normal cells are the same

• Run tests in scripts/r/binomtest: scripts/r/binomtest/run-test.R. This generates p-values for each tumor.

• This results are stored in results/bionmialTest/partial.

• To merge these results into one table, please run scripts/r/binomtest/merge-test-results.R.

• The results are stored in the results directory results/bionmialTest, in two formats: long and wide. The wide format with �tumors in columns are in results/bionmialTest/full-table-pvalues.csv.

Additionally, a table with statistics like median and mean expression level should be generated for normalized data.

• To do so, please run scripts/r/rsem-normalized/generate-tables.R. The results are stored in results/rsem-normalized/partial.

• Next run scripts/r/rsem-normalized/merge-tables.R to merge all partial results. The result is stored in results/rsem-normalized/full-table-long.csv and results/rsem-normalized/full-table.csv. Long and wide format respectively.

Heatmaps:

To generate data for heatmaps run:

• scripts/r/heatmap/generate-data.R - generates data based on the results of the binomial test and the stats of the normalized counts.

• scripts/r/heatmap/generate-plots.R - generates plots based on the data prepared in the previous step. All plots are generated in scripts/r/heatmap/plots