absorbance_read: Reading absorbance data from txt and csv files.

In jakehosen/stardom_aqualog: PARAFAC Analysis of EEMs from DOM

Description

Reading absorbance data from txt and csv files.

Usage

absorbance_read(absorbance_path, order = TRUE, recursive = TRUE,
  dec = NULL, sep = NULL, verbose = FALSE, ...)

Arguments

absorbance_path	directory containing absorbance data files or path to single file. See details for format of absorbance data.
order	logical, data is ordered according to wavelength
recursive	read files recursive, include subfolders
dec	optional, either you set a decimal separator or the table is tested for . and ,
sep	optional, either you set a field separator or it is tried to be determined automatically
verbose	logical, provide more information
...	additional arguments that are passed on to fread.

Details

If absorbance_path is a directory, contained files that end on "csv" or "txt" are passed on to read.table. If the path is a file, this file is read. Tables can either contain data from one sample or from several samples in columns. The first column is considered the wavelength column. A multi-sample file must have sample names as column names. All tables are combined to one with one wavelength column and one column for each sample containing the absorbance data. Column and decimal separators are guessed from the supplied data. In some cases, this can lead to strange results. Plaese set 'sep' and 'dec' manually if you encounter any problems.

Value

A data frame containing absorbance data. An attribute "location" contains the filenames where each sample was taken from.

See Also

fread

Examples

absorbance_path <- system.file("extdata", "absorbance", package = "staRdom")
absorbance <- absorbance_read(absorbance_path, verbose = TRUE)

jakehosen/stardom_aqualog documentation built on May 14, 2019, 3:06 a.m.