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'