DS additional modes - molgenis/systemsgenetics GitHub Wiki

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