check_input: Check input prior to processing in GCalignR

In GCalignR: Simple Peak Alignment for Gas-Chromatography Data

Check input prior to processing in GCalignR

Description

Checks input files for common formatting problems.

Usage

check_input(data, plot = FALSE, sep = "\t", message = TRUE, ...)

Arguments

data	Dataset containing peaks that need to be aligned and matched. For every peak a arbitrary number of numerical variables can be included (e.g. peak height, peak area) in addition to the mandatory retention time. The standard format is a tab-delimited text file according to the following layout: (1) The first row contains sample names, the (2) second row column names of the corresponding peak lists. Starting with the third row, peak lists are included for every sample that needs to be incorporated in the dataset. Here, a peak list contains data for individual peaks in rows, whereas columns specify variables in the order given in the second row of the text file. Peak lists of individual samples are concatenated horizontally and need to be of the same width (i.e. the same number of columns in consistent order). Alternatively, the input may be a list of data frames. Each data frame contains the peak data for a single individual. Variables (i.e.columns) are named consistently across data frames. The names of elements in the list are used as sample identifiers. Cells may be filled with numeric or integer values but no factors or characters are allowed. NA and 0 may be used to indicate empty rows.
plot	Boolean specifying if the distribution of peak numbers is plotted.
sep	The field separator character. The default is tab separated (sep = '\t'). See the "sep" argument in read.table for details.
message	Boolean determining if passing all checks is indicated by a message.
...	optional arguments passed to methods, see barplot.

Details

Sample names should contain just letters, numbers and underscores and no whitespaces. Each sample has to contain the same number of columns, one of which is the retention time and the others are arbitrary variables in consistent order across samples. Retention times are expected to be numeric, i.e. they are only allowed to contain numbers from 0-9 and "." as the only decimal character. Have a look at the vignettes for examples.

Author(s)

Martin Stoffel ([e-mail]) & Meinolf Ottensmann ([e-mail])

Examples

## gc-data
data("peak_data")
## Checks format
check_input(peak_data)
## Includes a barplot of peak numbers in the raw data
check_input(peak_data, plot = TRUE)

GCalignR documentation built on July 4, 2024, 1:07 a.m.