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