align {gcxgclab}

Reference Batch Align

Description

align aligns peaks from samples to a reference sample's peaks.

Usage

align(data_list, THR = 1e+05)

Arguments

data_list

a list object. Data extracted from each cdf file, ideally the output from extract_data().

THR

a float object. Threshold for peak intensity. Should be a number between the baseline value and the highest peak intensity. Default is THR = 100000.

Details

This function aligns the peaks from any number of samples. Peaks are aligned to the retention times of the first peak. If aligning to a reference or standard sample, this should be the first in the lists for data frames and for the mass data. The function comp_peaks() is used to find the corresponding peaks. This function will return a new list of TIC data frames and a list of mass data. The first sample's data is unchanged, used as the reference. Then a TIC data frame and mass data for each of the given samples containing the peaks and time coordinates of the aligned peaks. The time coordinates are aligned to the first sample's peaks, the peak height and MS is unchanged.

Value

A list object. List of aligned data from each cdf file and a list of peaks that were aligned for each file.

Examples

file1 <- system.file("extdata","sample1.cdf",package="gcxgclab")
file2 <- system.file("extdata","sample2.cdf",package="gcxgclab")
file3 <- system.file("extdata","sample3.cdf",package="gcxgclab")
frame1 <- extract_data(file1,mod_t=.5)
frame2 <- extract_data(file2,mod_t=.5)
frame3 <- extract_data(file3,mod_t=.5)
aligned <- align(list(frame1,frame2,frame3))
plot_peak(aligned$Peaks$S1,aligned$S1,title="Reference Sample 1")
plot_peak(aligned$Peaks$S2,aligned$S2,title="Aligned Sample 2")
plot_peak(aligned$Peaks$S3,aligned$S3,title="Aligned Sample 3")