ms_IDIT_QC: ms_IDIT_QC

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

Description

Function to generate a QC report for the ITDR or ITTR dataset

Usage

ms_IDIT_QC(
  data,
  foldername = NULL,
  reportname = NULL,
  nread = 10,
  simpleAUC = TRUE,
  PSMcutoff = TRUE,
  PSMthreshold = 3,
  isdatafitted = TRUE
)

Arguments

data	ITDR or ITTR dataset to perform QC analysis
foldername	name for the QC result folder
reportname	name for the QC report
nread	number of reading channels or sample treatements, default value 10
simpleAUC	whether to perform a simple calculation of AUC, default set to TRUE; note it is a bit "tricky" to interpret the AUC value in logarithmic space for most of ITDR data, suggest to just use simpleAUC by default
PSMcutoff	whether to apply PSM threshold cutoff on hit selection, default set to TRUE
PSMthreshold	the threshold of averaged PSM numbers to consider protein quantification as reliable, default value is 3
isdatafitted	whether the provided data is associated with fitting parameters, i.e., after ms_ITDR_fitting or ms_ITTR_fitting

Examples

## Not run: 
ms_IDIT_QC(ITDRdata_fitted)
ms_IDIT_QC(ITDRdata_scaled, isdatafitted=FALSE, foldername="QC1")

## End(Not run)

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