dot-filterByScore: Filter PSMs / proteins by a given score column.

In MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

Description

Filter PSMs / proteins by a given score column.

Usage

.filterByScore(
  input,
  score_column,
  score_threshold,
  direction,
  behavior,
  handle_na = "keep",
  fill_value = NA,
  filter = TRUE,
  drop = TRUE
)

Arguments

input	data.table preprocessed by one of the .cleanRaw* functions.
score_column	chr, name of the column that contains scores.
score_threshold	num, values below or above this threshold will be removed from the data.
direction	chr, if "greater" only values above the threshold will be retained, if "smaller" - below the threshold.
behavior	chr, if "remove", values below/above the threshold will be removed, if "replace", they will be set to fill_value.
fill_value	if behavior = "replace", values below/above the threshold will be replaced with fill_value. Defaults to NA.
filter	If TRUE, filtering will be performed.
drop	if TRUE, score_column will be removed.

Value

data.table

MSstatsConvert documentation built on Nov. 8, 2020, 5:49 p.m.