sig_gseapreranked_tool

Run pre-ranked GSEA on a ranked matrix

Synopsis

sig_gseapreranked_tool [--up, --uptag UP] [--score SCORE] [--rank RANK] [--sig_meta SIG_META] [--metric METRIC] [--es_tail ES_TAIL] [--num_perm NUM_PERM] [--query_meta QUERY_META] [--save_minimal SAVE_MINIMAL] [--save_digests SAVE_DIGESTS] [--max_col MAX_COL]

Arguments

--up, --uptag UP : Geneset(s) to use for the up portion of the query

--score SCORE : Custom dataset of differential expression scores (e.g. zscores) in GCT(X) format. Use in combination with rank parameter.

--rank RANK : Custom dataset of ranks corresponding to the score matrix in GCT(X) format. Use in combination with score parameter.

--sig_meta SIG_META : Signature metadata for each column in the score matrix. This is a required field. The first field must match the column id field in the score matrix.

--metric METRIC : Similarity metric. Default is wtcs. Options are {wtcs|cs}

--es_tail ES_TAIL : Specify direction of one-tailed statistic for enrichment metrics. Default is up. Options are {up|down}

--num_perm NUM_PERM : Number of null permutations per unique set size. Default is 500

--query_meta QUERY_META : Metadata for each query.

--save_minimal SAVE_MINIMAL : Save minimal output to optimize storage requirements. For enrichment based metrics only the combined scores are saved. Default is 1

--save_digests SAVE_DIGESTS : Save per-query digests. Default is 1

--max_col MAX_COL : Maximum number of columns of the score/rank matrices to read at a time. Default is 25000

Description

The tool computes set-based enrichment analysis against a user-defined rank-ordered dataset. It determines whether a priori defined sets show statistically significant enrichment at either end of the ranking.

Examples

• Run preRanked GSEA

sig_gseapreranked_tool --up 'up.gmt' --score 'score.gctx'