find_geneExp4block

Find differential gene expression for mutation blocks.

Optional Arguments:

  • -h, –help: Show this help message and exit.

Required Arguments:

  • -in_BGfolder IN_BLOCKS_GENOME_FOLDER, –in_blocks_genome_folder IN_BLOCKS_GENOME_FOLDER: Path of blocks mapped to genomic region files, which are exported by map_block2genome.

  • -in_SBfile IN_SORTEDBLOCK_FILE, –in_sortedBlock_file IN_SORTEDBLOCK_FILE: Bpb3 exported mutation block summary position file in BED format and sorted by chromosome and position.

  • -in_DGfile IN_DEG_FILE, –in_deg_file IN_DEG_FILE: A differentially expressed gene file in tab delimited format, which is an export file from bpb3 differential_expression.

  • -out_folder OUT_FILE_FOLDER, –out_file_folder OUT_FILE_FOLDER: Path of file folder to export results.

Optional Arguments with Default Values:

  • -in_FTlist, –in_feature_list: A comma-separated string representing features of genomic regions that will be considered. Default=TSS,gene,TES,5dist,enhancers, where each feature is separated by a comma.

  • -in_cutoff IN_DMR_MINIMUM_CUTOFF, –in_dmr_minimum_cutoff IN_DMR_MINIMUM_CUTOFF: Minimum cutoff values for selecting blocks or mrs to export. Default=None, which means no minimum cutoff for exporting data or there is no 9th column (p-value or other values can be used to filter by minimum cutoff) in the dataframe.