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sig_introspect_tool

Compute internal connectivities between signatures

Synopsis

sig_introspect_tool [--sig_score SIG_SCORE] [--sig_rank SIG_RANK] [--sig_connectivity SIG_CONNECTIVITY] [--sig_col_meta SIG_COL_META] [--bkg_connectivity BKG_CONNECTIVITY] [--bkg_row_meta BKG_ROW_META] [--gset_size GSET_SIZE] [--metric METRIC] [--es_tail ES_TAIL] [--rid RID] [--row_space ROW_SPACE] [--symmetricize_result SYMMETRICIZE_RESULT] [--max_el MAX_EL] [--use_gctx USE_GCTX]

Arguments

--sig_score SIG_SCORE : Input signature scores

--sig_rank SIG_RANK : Ranks of input signatures

--sig_connectivity SIG_CONNECTIVITY : Pre-computed self query results.

--sig_col_meta SIG_COL_META : Alternative column annotations for the signature score matrix. Must include column id, pert_type and cell_id as a minimum. The column id field must be the first column or be named id.

--bkg_connectivity BKG_CONNECTIVITY : Pre-computed query results (e.g. wtcs scores) using identical genesets against the designated background signatures. Note for proper interpretation, the query metric and parameters used here must match those supplied to introspect.

--bkg_row_meta BKG_ROW_META : Alternative row annotations for background connectivity matrix. Must include row id, pert_type and cell_id as a minimum. The row id field must be the first column or be named id.

--gset_size GSET_SIZE : Length of genesets to use for enrichment metrics. Default is 50

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

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

--rid RID : List of row ids to to use specified as a GRP file or cell array. If empty all rows are used

--row_space ROW_SPACE : Common row-id space definitions to use as an alternative to the rid parameter. Default is all. Options are {all|lm|bing|aig|lm_probeset|bing_probeset|full_probeset|custom}

--symmetricize_result SYMMETRICIZE_RESULT : Make the result matrices symmetric by averaging the values with their transpose.. Default is 1. Options are {1,0}

--max_el MAX_EL : Maximum number of elements to read at a time. Default is 2.5e+08

--use_gctx USE_GCTX : Save results in binary GCTX format if true, text GCT format if false. Default is 1

Description

The introspect analysis examines the similarities between a group of gene expression signatures. It takes a matrix of signatures as input and computes similarities between, them adjusting the strength of connectivities using all the signatures or a pre-computed connectivity matrix as a background distribution.

It does this by first executing queries of the signatures against one another. Different similarity metrics of similarity are supported, see sig_query_tool for a description of the metrics. Next the similarity scores are normalized i.e. adjusted for co-variates of perturbagen type and cell line identity. Finally the scores are converted to percentile scores using a user-specified signature set as a null distribution.

Examples

  • Run introspect using the signature matrix as the background

sig_introspect_tool --sig_score 'sig_zscore.gct'

  • Run introspect using a pre-computed background

sig_introspect_tool --sig_score 'sig_zscore.gct --bkg_connectivity 'bkg_wtcs.gct'

  • Run introspect using pre-computed introspect and background results

sig_introspect_tool --sig_connectivity 'sig_wtcs.gct' --bkg_connectivity 'bkg_wtcs.gct'