ms_select_goodmeltcurve: ms_select_goodmeltcurve

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

Description

Function to perform good quality melting curve selection on dataframe The main criteria including averaged R2>0.8, with steady plateau at the top and bottom parts of the melting curves. It could be better to use the fitted reading instead of raw readings (TBA)

Usage

ms_select_goodmeltcurve(
  data,
  nread = 10,
  ctrlcondition = NULL,
  checkTm = TRUE,
  stableplateau = TRUE,
  topCVcutoff = 0.1,
  bottomCVcutoff = 0.1,
  topcutoff = NULL,
  bottomcutoff = NULL,
  nMAD = 2.5,
  reverse = FALSE
)

Arguments

data	dataset to look for complete set
nread	number of reading channels or sample treatements, default value is 10
ctrlcondition	by default the function only apply on the Control treatment data with specified condition keyword "Ctrl"/"DMSO", the user could add additional customized condition keyword using this argument
checkTm	whether check Tm is valid ie, not NA value
stableplateau	whether to select the protein with properly stable plateau in the melt curve, default set to TRUE
topCVcutoff	the threshold CV value used to define the top plateau cutoff, default value is 0.1
bottomCVcutoff	the threshold CV value used to define the bottom plateau cutoff, default value is 0.1
topcutoff	the threshold value to control the minimal top plateau, when provided
bottomcutoff	the threshold value to control the maximal bottom plateau, when provided
nMAD	when top or bottom CV cutoff were not provided, the cutoff value would be determined using MAD scheme, nMAD indicates the significance level of MAD cutoff, default value is 2.5
reverse	whether to return the to-be-removed bad melt curves, default set to FALSE

Value

dataframe containing the subset of melting curves with good melting profile

Examples

## Not run: 
data_good <- ms_select_goodmeltcurve(data_scaled, bottomcutoff=0.3)

## End(Not run)

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