Description Usage Arguments Details Value Examples
MSThermExperiment
creates a new experiment object from
a set of filenames or data frames.
1 | MSThermExperiment(control, annotations)
|
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 |
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):
Unique identifier of a single replicate
Sample name that a replicate belongs to
Path to file on disk containing the quantification data
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:
Sequence of the matched peptide in single-letter IUPAC
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):
Calculated precursor co-isolation interference (0.0-1.0)
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)
An MSThermExperiment object
1 2 3 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.