ms_isoform_consolidate: ms_isoform_consolidate

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

Description

Function to perform isoform ambiguity cleanup step 2 using the principle of parsimony when two or more isoforms are identified within the same search result dataset

Usage

ms_isoform_consolidate(
  data,
  matchtable,
  nread = 10,
  withabd = FALSE,
  weightbycountnum = TRUE
)

Arguments

data	dataset to be clead-up from isoform ambiguity
matchtable	an isoform substitution matching table
nread	number of reading channels or sample treatements, default value 10
withabd	whether the dataset contains abundance data as in ITDR/ITTR data, by default set to FALSE
weightbycountnum	by default to consolidate the isoforms

Details

Note: Data must contain "sumUniPeps","sumPSMs","countNum" columns, otherwise the mock named columns should be provided.

Value

a dataframe

Examples

## Not run: 
data_cleaned2 <- ms_isoform_consolidate(data_cleaned1,
              matchtable="./subfolder/tobe_consolidated.txt")
data_cleaned2 <- ms_isoform_consolidate(data_cleaned1,
              matchtable="./subfolder/tobe_consolidated.txt", withabd=TRUE)

## End(Not run)

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