MSupload: Upload MSdata

In flajole/MSdata: Mass-spectrometry data analysis package

Description

Create a MSdata-class object from external data tables. Automatically adds a ReplicationGroup column in sampleData table according to group factors combinations. #' Remember that in file paths you should use either "/" or double "\", not just "\".

Usage

MSupload(object, ...)

## S4 method for signature 'character'
MSupload(object, orientation = "SamplesInCol",
  zeros.as.NA = TRUE, sampleDataLines = 1, peakDataLines = 1,
  sampleNames = TRUE, peakNames = TRUE)

## S4 method for signature 'list'
MSupload(object = list(intFile = "", sampleFile = "",
  peakFile = ""), orientation = "SamplesInCol", zeros.as.NA = TRUE)

Arguments

object	One of: a character vector of length 1 - just a file path name of one .csv or .txt data frame. a list of paths to three files: matrix of intensities, sample metadata and peak metadata.
orientation	Orientation of table, one of "SamplesInCol" or "SamplesInRow"
zeros.as.NA	If TRUE then zero intensities are treated as NAs.
sampleDataLines	The number of lines containing data about samples.
peakDataLines	The number of lines containing data about peaks/compounds.
sampleNames	If TRUE, sample names are taken from the first column/row of table. If FALSE, standard names like "sample1" are created.
peakNames	If TRUE, sample names are taken from the first row/column of table. If FALSE, standard names like "peak1" are created.

Value

MSdata-class object

Methods (by class)

• character: Upload intensity matrix with several lines of peak and sample metadata.

• list: Upload intensity matrix, sample data, peak data separately

flajole/MSdata documentation built on May 16, 2019, 1:17 p.m.