minCountConstraint.DataFilter: Perform minimum count based thresholding of an input vector

In IdMappingAnalysis: ID Mapping Analysis

Description

Perform minimum count based thresholding of an input vector.

Usage

## Static method (use this):
## DataFilter$minCountConstraint(x, filtParams, ...)

## Don't use the below:
## S3 method for class 'DataFilter'
minCountConstraint(static, x, filtParams, ...)

Arguments

x	numeric input vector.
filtParams	vector of constraint parameters. If the fraction of input elements which value is greater or equal filtParams[1] is less than filtParam[2], the whole vector is replaced be NA vector of the same length.
...	Not used

Value

numeric vector or vector of NA 's depending on thresholding criteria.

Author(s)

Alex Lisovich, Roger Day

See Also

For more information see DataFilter.

Examples

 #set to NA protein count rows which contain less than 50 percent of counts >=2
 fltExperimentSet<-DataFilter$do.apply(examples$msmsExperimentSet,
   byRows=TRUE,filterFun=DataFilter$minCountConstraint,filtParams=c(2,0.5),verbose=TRUE);

 #print the number of rows set to NA
 sum(is.na(rowSums(fltExperimentSet[,-1])))
 

IdMappingAnalysis documentation built on Oct. 31, 2019, 3:30 a.m.