Skip to content

SigSliceTool

Extract a subset from a larger dataset

Synopsis

SigSliceTool [--ds DS] [--cid CID] [--rid RID] [--row_space ROW_SPACE] [--row_meta ROW_META] [--col_meta COL_META] [--use_gctx USE_GCTX] [--num_digits NUM_DIGITS] [--ignore_missing IGNORE_MISSING]

Arguments

--ds DS : Dataset in GCT or GCTX format

--cid CID : List of column ids to extract as a GRP file or cell array.

--rid RID : List of row ids to extract as a GRP file or cell array

--row_space ROW_SPACE : Common row-id spaces to extract. '_probeset' refers to affy ids. Default is custom. Options are {lm|lm_probeset|bing|bing_probeset|aig|full_probeset|custom}

--row_meta ROW_META : Row metadata as a TSV text file. If provided the rows in the output dataset will be annotated using the first field as the key to join with the row-ids

--col_meta COL_META : Column metadata as a TSV text file. If provided the columns in the output dataset will be annotated using the first field as the key to join with the column-ids

--use_gctx USE_GCTX : Save results in GCTX format if true or GCT otherwise. Default is 1

--num_digits NUM_DIGITS : Number of digits to use when writing to GCT format. Default is 4

--ignore_missing IGNORE_MISSING : If false, program will fail when missing any specified rids or cids. Default is 0

Description

This tool extracts a subset of rows and columns from a larger dataset.

Examples

  • Extract a subset of columns from a larger dataset

sig_slice_tool --ds 'data.gctx' --cid 'column_ids.grp' --rid 'row_ids.grp'

  • Extract only landmark genes for a subset of columns

sig_slice_tool --ds 'data.gctx' --cid 'columns.grp' --row_space lm