scHPF score

Basic usage

To get gene- and cell-scores in a tab-delimited file, ordered like the genes and cells in the train file and with a column for each factor:

scHPF score -m MODEL_JOBLIB -o OUTDIR -p PREFIX

To also generate a tab-delimited file of gene names, ranked by gene-score for each factor:

scHPF score -m MODEL_JOBLIB -o OUTDIR -p PREFIX -g GENE_FILE

GENE_FILE is intended to be the gene.txt file output by the scHPF prep command, but can in theory be any tab-delimited file where the number of rows is equal to the number of genes in the scHPF model. The score command automatically uses the 1st (zero-indexed) column of GENE_FILE (or the only column if there is only one); however, the column used can be specified with --name-col.

If OUTDIR is omitted, the command will make a new subdirectory of the directory containing the model. The new subdirectory will have the same name as the model file, but without the joblib extension.

The command also outputs files which can be used to select the number of factors using trained models.

Complete options

For complete options, see the complete CLI reference or use the -h option on the command line:

scHPF score -h