Skip to content

DS additional modes

Patrick Deelen edited this page Sep 21, 2021 · 6 revisions

Below are the different modes of Downstreamer. For an overview of the default workflow please see: Downstreamer ewqrewqrwq

Mode Description
STEP1 Run the Downstreamer prioritization.
STEP2 Run the Downstreamer prioritization starting at stage 2.
CONVERT_TXT Convert a txt z-score matrix to binary. Use --gwas, --output and optionally --pvalueToZscore if the matrix contains p-values instead of z-scores.
CONVERT_TXT_MERGE Merge multiple txt pvalue files into one matrix containing only overlapping snps
CONVERT_BIN Convert a binary matrix to a txt. Use --gwas and --output optionally --columnsToExtract
CONVERT_EXP Convert a tab separated expression matrix and normalize genes. Use --gwas (for exp data) and --output optionally --columnsToExtract
TRANSPOSE Transposes a binary matrix. Use --gwas and --output
CONVERT_EQTL Convert binary matrix with eQTL z-scores from our pipeline. Use --gwas and --output
CONVERT_GTEX Convert Gtex median tissue GCT file. Use --gwas for the GCT file and --output
CORRELATE_GENES Create gene correlation matrix with 0 on diagonal. Use --gwas as input matrix (genes on row, tab separated), --output and --genes. Optionally use --corZscore to create Z-score matrix
R_2_Z_SCORE Convert correlation matrix with r values to Z-score matrix. Must be used together with -ns
MERGE_BIN Merge multiple bin matrix on overlapping rows
Clone this wiki locally