ms_ITDR_filter: ms_ITDR_filter

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

Description

Function to perform ITDR data segregation and positive hits selection based on desired fc threshold level and the associated fitting parameters

Usage

ms_ITDR_filter(
  data,
  nread = 10,
  checkpointposition = NULL,
  fcthreshold = 0.3,
  R2threshold = 0.8,
  baselineMAD = 0,
  nbaseline = 3,
  nMAD = 2.5,
  checkreplicate = TRUE,
  treatcondition = NULL,
  PSMcutoff = TRUE,
  PSMthreshold = 3
)

Arguments

data	dataset to be filtered
nread	number of reading channels or sample treatements, default value is 10
checkpointposition	refering to the positions of dose points to check whether their readings surpass fcthreshold, default value is NULL, which would automatically check the highest 3 dose points
fcthreshold	short for fold change threshold, indicate the threshold fold change compared to baseline (i.e.,1.0) above which the readings can be considered significantly stabilized or destabilized, default value is 0.3
R2threshold	minimal R2 to consider dose-reponse fitting as reliable
baselineMAD	MAD of baseline variation, default value is 0; if not provided, it will be calculated based on the readings from the lowest few dose points, specified by nbaseline value
nbaseline	the number of points (count from lowest concentration) used for calculate the baseline MAD, default is 3
nMAD	the significance level of MAD cutoff, default value is 2.5
checkreplicate	whether to check replicated measurements, when set to TRUE, further segregate the proteins that all the replicated measurements from at least one experimental condition surpass fold change threshold, default set to TRUE
treatcondition	specify the condition names to perform replicate check, no need to specify the replicate part of the full condition names, useful when multiple experimental conditions are contained in the dataset
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

Value

a list of segregated dataframes

Examples

## Not run: 
ITDRdata_filtered <- ms_ITDR_filter(ITDRdata_fitted, fcthreshold=0.3,
                     checkreplicate=TRUE, PSMcutoff=TRUE)

## End(Not run)

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