import_identifications: Import protein identification data

In mstaniak/SharedPeptides: Handle Shared Peptides in Mass-Spectrometry-based Proteomics

Description

Import protein identification data

Usage

import_identifications(identifications, columns, score_control = NULL, ...)

## S3 method for class 'character'
import_identifications(identifications, columns, score_control = NULL, ...)

## S3 method for class 'data.frame'
import_identifications(identifications, columns, score_control = NULL, ...)

Arguments

identifications	a character string or a data.frame. In the first case, it will be treated as path to a delimited file that will be imported via the 'read.delim' function. In the second case, the data.frame will processed by selecting relevant columns and optional filtering.
columns	a named list of two to four elements that describe columns in input data. 'peptides' element identifies a colums that correspond to identified peptides, 'proteins' - to proteins. Field 'intensities' can be specified if abundance data are included. Field 'grouping_variables' can be added if any of the columns of the input define a grouping. Operations on the output can then be performed in groups.
score_control	a named list of three elements that describe optional filtering of the data by a chosen PSM-quality metric. Element 'score_column' names the column of metric scores, 'threshold' is a numeric cut-off point for this metric and 'direction' ("greater"/"smaller") tells if the scores should be greater or smaller than the threshold.
...	these optional parameters will be passed to the 'read.delim' function if the first parameter is a path to a file.

Value

data.frame of class 'shared_peptides_identifications'.

Methods (by class)

• character: 'identifications' parameter is treated as a path to a delimited file.

• data.frame: the 'identifications' parameter is treated as a 'data.frame' with peptide-spectrum matches.

Examples

df <- data.frame(peptide = c('AA', 'AAA'), protein = c('P1', 'P1,P2'))
import_identifications(df, list(peptides = 'peptide', proteins = 'protein'))

mstaniak/SharedPeptides documentation built on Jan. 21, 2020, 7:29 p.m.