Description Usage Arguments Value Methods (by class) Examples
Import protein identification data
1 2 3 4 5 6 7 | 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, ...)
|
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. |
data.frame of class 'shared_peptides_identifications'.
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.
1 2 | df <- data.frame(peptide = c('AA', 'AAA'), protein = c('P1', 'P1,P2'))
import_identifications(df, list(peptides = 'peptide', proteins = 'protein'))
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