normalize

Normalizes the data (entities, for instance genes or proteins) by column (samples). Can read stdin.

normalize, Gregory W. Schwartz. Normalizes the data (entities, for instance
genes or proteins) by column (samples). Can read stdin.

Usage: normalize [--labelField TEXT] --sampleField TEXT --entityField TEXT
                 --valueField TEXT [--entityDiff TEXT] [--bySample TEXT]
                 [--bySampleRemoveSynonyms] [--method STRING]
                 [--filterEntitiesMissing INT] [--filterEntitiesValue DOUBLE]
                 [--filterEntitiesStdDev DOUBLE] [--base DOUBLE]

Available options:
  -h,--help                Show this help text
  --labelField TEXT        The column containing the label for the entry.
  --sampleField TEXT       The column containing the sample for the entry.
  --entityField TEXT       The column containing the id for the entity in the
                           entry.
  --valueField TEXT        The column field containing the value for the entry.
  --entityDiff TEXT        When comparing entities that are the same, ignore the
                           text after this separator. Used for the bySample
                           normalization. For example, if we have a strings
                           ARG29_5 and ARG29_7 that we both want to be divided
                           by another entity in another sample called ARG29, we
                           would set this string to be "_"
  --bySample TEXT          Normalize as usual, but at the end use this string to
                           differentiate the sample field from the normalization
                           samples, then divide the matching samples with these
                           samples and renormalize. For instance, if we want to
                           normalize "normalizeMe" by "normalizeMeByThis", we
                           would set this string to be "ByThis" so the
                           normalized values from "normalizeMe" are divided by
                           the normalized values from "normalizeMeByThis". This
                           string must make the latter become the former, so
                           "By" would not work as it would become
                           "normalizeMeThis". If there is no divisor, we remove
                           that entity.
  --bySampleRemoveSynonyms When normalizing by sample, if the divisor appears
                           multiple times we assume those are synonyms. Here, we
                           would remove the synonym with the smaller intensity.
                           If not set, errors out and provides the synonym name.
  --method STRING          ([StandardScore] | UpperQuartile | None) The method
                           for standardization of the samples.
  --filterEntitiesMissing INT
                           ([0] | INT) Whether to remove entities that appear
                           less than this many times after normalizing.
  --filterEntitiesValue DOUBLE
                           ([Nothing] | DOUBLE) Whether to remove entities in
                           filterEntitiesMissing but also counting entities with
                           a value of this or less as missing.
  --filterEntitiesStdDev DOUBLE
                           ([Nothing] | DOUBLE) Remove entities that have less
                           than this value for their standard deviation among
                           all samples they appear in, after normalization.
  --base DOUBLE            ([Nothing] | DOUBLE) Log transform the data at the
                           end using this base but before filtering.