sig_score2rank_tool¶
Generate rank matrix from score matrix
Synopsis¶
sig_score2rank_tool
[--ds DS] [--outfile
OUTFILE] [--dim DIM] [--sort_order SORT_ORDER] [--ignore_nan IGNORE_NAN] [--as_fraction
AS_FRACTION] [--as_percentile AS_PERCENTILE] [--fix_ties FIX_TIES] [--use_gctx USE_GCTX]
[--read_mode READ_MODE] [--block_size BLOCK_SIZE]
Arguments¶
--ds
DS
: Input score matrix to compute ranks
--outfile
OUTFILE
: Output filename of rank matrix.
--dim
DIM
: Dimension to operate on. Default is column. Options are {column|row}
--sort_order
SORT_ORDER
: Sort order. Default is descend. Options are {descend|ascend}
--ignore_nan
IGNORE_NAN
: Ignore NaNs when ranking. Note that ignoring NaNs is slower. Default is 1
--as_fraction
AS_FRACTION
: Logical, returns ranks as a fraction of total rows. Default is 0
--as_percentile
AS_PERCENTILE
: Logical, returns ranks as a percentile of total rows. Default is 0
--fix_ties
FIX_TIES
: Logical, adjusts for ties (is false by default). Default is 0
--use_gctx
USE_GCTX
: Use GCTX file format. Default is 1
--read_mode
READ_MODE
: Specify how to process the input matrix. If full is specified the complete
matrix is processed enmasse. If iterative the input matrix is processed in
blocks. Default is full. Options are {full|iterative}
--block_size
BLOCK_SIZE
: size of blocks to process if the read_mode is iterative. Default is 50000
Description¶
Rank orders the input dataset along dimension dim
in the order specified by sort_order
. The rank matrix is used by connectivity analysis tools such as queryl1k to speed up the computation of enrichment based similarities.
Examples¶
- Calculate ranks of input score matrix
sig_score2rank_tool --ds 'raw_data.gctx'