mstherm (version 0.4.7)

MSThermExperiment: Create a new MSThermExperiment.

Description

MSThermExperiment creates a new experiment object from a set of filenames or data frames.

Usage

MSThermExperiment(control, annotations)

Arguments

control

data frame or filename of tab-delimited table describing the experimental setup and locations of data on disk (see Details)

annotations

data frame or filename to tab-delimited table containing protein names and annotations (usually functional descriptions but can be any text

Value

An MSThermExperiment object

Details

Both parameters can take either a data frame or a tab-delimited filename on disk (which will be read into a data frame). "control" should contain columns with the following headers (in any order):

"name"

Unique identifier of a single replicate

"sample"

Sample name that a replicate belongs to

"data_file"

Path to file on disk containing the quantification data

"meta_file"

Path to file on disk containing the labeling metadata

The "meta_file" should be tab-delimited text and contain two columns labeled "channel" and "temp". The "data_file" should be tab-delimited text and contain, at a minimum, the following columns:

"peptide"

Sequence of the matched peptide in single-letter IUPAC

"protein"

Protein or protein group to which the peptide belongs

"..."

One column per isobaric channel, containing absolute quantification values. Column names must match those in the "channel" column of the meta file, with the exception that R will automatically convert any name not compatible with its syntax rules. To be safe, use only letters, digits, underscores, and periods in channel names and never start with a digit (e.g. use "TMT.126" rather than "126")

The following columns can also be utilized for filtering if included (all others will simply be ignored):

"coelute_inf"

Calculated precursor co-isolation interference (0.0-1.0)

"score"

Score assigned by the processing software to the PSM

"annotations" should contain two columns with the headers "name" and "annotation". "name" should match the protein names in the data files, and "annotation" can contain any text (generally a functional description)

Examples

control <- system.file("extdata", "demo_project/control.tsv", package="mstherm")
annots  <- system.file("extdata", "demo_project/annots.tsv",  package="mstherm")
expt    <- MSThermExperiment(control, annotations=annots)