++ed by:
ZMUGHAL

1 PAUSE user

Emmanouil "Manolis" Maragkakis
and 1 contributors

NAME

CLIPSeqTools::CompareApp::compare_counts - Compare tables with counts.

SYNOPSIS

clipseqtools compare_counts [options/parameters]

DESCRIPTION

Do Upper Quartile normalization on specified value column of one or more tables. For each table, all entries are sorted by descending value (specified by val_col). All values are divided by the value of the 25%th entry. The 25%th entry is specified by the table with the fewer entries after the entries with value lower than val_thres in all tables are excluded.

OPTIONS

  Input options.
    --table <Str>          input table file/files. Use option multiple
                           times to specify multiple table files.
    --t_name <Str>         table name. Use option multiple times to give names
                           to all the tables. The number of table names must
                           match the number of input table files. If not set,
                           numbers are used instead. These names will be used
                           in the output files.
    --key_col <Str>        name for the column/columns to use as a key. It
                           must be unique for each table row. Use option
                           multiple times to specify multiple columns.
    --val_col <Str>        name of column with values to be normalized.

  Output.
    --o_table <Str>        output table file/files. Use option multiple
                           times to give multiple files. Must be given as
                           many times as the table option.

  Other options.
    --val_thres <Num>      rows with value lower or equal than val_thres
                           are not used for normalization. Default: 0
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message