filterDEG4bpb3

This command is used to filter Differential Expressed Genes (DEG) by rratio based on the exported file from bpb3 differential_expression. It exports the filtered DEG with group mean and rratio.

Optional arguments:

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

Required arguments for filtering:

  • –in_group1_str NAME: Group1 column label.

  • –in_group2_str NAME: Group2 column label.

  • –in_folder FILE_FOLDER: Input file folder that contains the bpb3 exported differential expression gene file.

  • –in_file FILE_NAME: Input file name of the bpb3 exported differential expression gene file.

Optional arguments for filtering (with default values):

  • –min_median_RPKM NUMBER: Minimum median of RPKM value in each group. Default value is 1.0. If it is smaller than 0, this option will be switched off.

  • –rr_cutoff NUMBER: Cutoff value for rratios to filter differential expression genes between two groups. Default value is 0.18. rr>0.14, 0.18, 0.22, 0.4, 0.67 represent 1.15, 1.2, 1.25, 1.5, 2.0 folder changes, respectively.

  • –sort_by_column_str NAME: Column name of the dataframe column that will be sorted after filtering. Default value is differential_expressoin_T_test_p_value if the file is obtained from the bpb3 package.

  • –is_median: Use mean or median of group values to calculate folder changes between groups. Default value is False, which uses the mean value of the group.

Please replace the angle-bracketed placeholders (<>) with appropriate values when using the command.