ms_clean: ms_clean

In nkdailingyun/mineCETSA: Processing and Visualization of Proteome-wide MS-CETSA data

Description

Function to clean up read-in dataset, mainly to remove not-quantified entries

Usage

ms_clean(
  data,
  nread = 10,
  remkeratin = TRUE,
  remserum = TRUE,
  remtrypsin = TRUE,
  remsinglecondprot = FALSE
)

Arguments

data	dataset to be cleaned up
nread	number of reading channels or sample treatements, default value 10
remkeratin	whether to remove Keratin protein, which is generally considered as a common contaminant, default set to TRUE
remserum	whether to remove Serum albumin protein, which is generally considered to be from culture medium, default set to TRUE
remtrypsin	whether to remove trypsin protein, which is generally considered to be from digestion reaction, default set to TRUE
remsinglecondprot	whether the orphan proteins that appear only in one of the datasets should be removed, default set to FALSE

Value

a dataframe after clean-up

Examples

## Not run: 
 ITDRdata_cleaned <- ms_clean(ITDRdata)

## End(Not run)

nkdailingyun/mineCETSA documentation built on Feb. 27, 2021, 8:26 p.m.