readFTICR: Read in chuncks of an FT-ICR-MS file

In ktoddbrown/FTICR_Processing: R package for post-processing of FT-ICR-MS data with a focus on organic carbons

Description

Read in chuncks of an FT-ICR-MS file

Usage

readFTICR(fileIn, massHeader, sampleRegStr = NULL, samplesToRead = NULL,
  elementKey = NULL, verbose = FALSE)

Arguments

fileIn	a string identifying the csv file to read our FT-ICR-MS data from
massHeader	an array of strings or single string naming the mass to charge header
sampleRegStr	a regular expression matching the sample headers (and ONLY the sample headers)
samplesToRead	an array of indecies or regular expression or array of names of the samples to be read in
verbose	boolean flag for verbose outputs

Value

a data frame with the long table format with the mass ID, sample ID, and intensity

Examples

##read samples by index (note this is the Nth sample not the Nth column)
#readFTICR(fileIn='testfile.csv', samplesToRead=1:2)
##read samples by regular expression match of sample name
#readFTICR(fileIn='testFile.csv', samplesToRead='out2\\d')
##read samples by matched name
#readFTICR(fileIn='testFile.csv', samplesToRead=c('X.out20', 'X.out21'))

ktoddbrown/FTICR_Processing documentation built on May 20, 2019, 7:05 p.m.