read.metfile: Read metabolomics data

In liucaomics/genuMet: distinguish genuine signal of untargeted metabolites from measurement artifacts without QC samples

Description

read.metfile read in a standard metabolomics dataset in csv format. The input table can be partitioned into 4 rectangular region. The top left is blank. The top right is row headers. The down left is column headers. The down right is metabolites signal matrix, whose columns are samples in injection order and rows are metabolites.

Usage

read.metfile(filename, nrowheader = 4, ncolheader = 7, metcol = 1,
  smplrow = 4, resmpl = "")

Arguments

nrowheader	Number of row headers in the file. Default is 4.
ncolheader	Number of column headers in the file. Default is 7.
metcol	Column index of the metabolites ID. Default is 1.
smplrow	Row index of the sample ID. Default is 4.
resmpl	Regular expression of the sample IDs to be analyzed (which is used in grepl). Default includes all the samples.
file	Name of cvs file of the metabolomics dataset.

Value

A data frame of metabolites signal. Each row is a metabolite and each column is a sample.

Author(s)

Liu Cao

liucaomics/genuMet documentation built on Nov. 11, 2019, 12:13 a.m.