scScoreFeatures

scScoreFeatures#

scScoreFeatures aggregated region-level signal in a pre-processed .h5ad object into gene-level scores based on a user-provided BED/GTF file.

usage: 
scScoreFeatures -i INPUT_binned.h5ad --features <bed or gtf> -o OUTPUT_scores.h5ad

Input/Output options#

--input, -i

sincei-generated input file in .h5ad format.

--outFile, -o

The file to write results to. For scFilterStats, scFilterBarcodes and scJSD, the output file is a .tsv file. For other tools, the output file is an updated .h5ad file with the result of the requested operation.

Common Options#

--features, -f

Path to the BED or GTF file containing the features to use for aggregation/scoring.

--overlapPolicy, -op

Possible choices: partial, all, none

Policy for handling regions present in .h5ad input file that only partially overlap regions present in --features. Options are:

  • partial: count reads in anndata regions proportionally to the overlap fraction,(counts_considered = feature_counts * overlap_length / region_length).

  • all: count all reads in the partially overlapping anndata regions.

  • none: Only count reads in anndata regions that are fully contained within BED/GTF regions.

Default: 'partial'.

--centerScores, -cs

If flag is set, center and scale the scores to unit variance and zero mean. Default: False.

--numberOfProcessors, -p

Number of processors to use. Type "max/2" to use half the maximum number of processors or "max" to use all available processors. Default: "max".

--bedScoreFilter, -bsf

Provide a range (two values separated by space), or a threshold (upper limit) of score to determine which input features to consider for scoring. Used only when the input is a BED file containing scores (stored in the 5th column). Default: None.

--maxRegion, -mr

Maximum region size (in kb) upstream and downstream of the genes to consider for activity calculation. Default: 100.

--normalizeGeneLengths

Flag to indicate whether to apply length normalization to the input genes. If provided, gene scores are normalized w.r.t. gene length in the input GTF/BED file. Default: False.

Other options#

--verbose, -v

Set to see processing messages.

-V, --version

Print the program version and exit.