Description Usage Arguments Value Author(s) See Also Examples
Changes accessions from one protein id to another.
1 2 3 4 5 6 | remap_accessions(object,
conversion_table,
extraction_pttrn=c("\\|([^|-]+)(-\\d+)?\\|",
"([A-Z]P_\\d+)",
"(ENS[A-Z0-9]+)"),
path_to_FASTA=NULL)
|
object |
An instance of class "MSnID". |
conversion_table |
(data.frame) first column in the data frame corresponds to identifiers in the FASTA file. Second column is the new identifier. |
extraction_pttrn |
(string) regex pattern that extract protein identifier from
FASTA entry name as first group (that is |
path_to_FASTA |
(string) path to FASTA file. If provided only accessions present in the given FASTA file will be retained. |
Returns an instance of "MSnID" with updated accessions
.
Vladislav A Petyuk vladislav.petyuk@pnnl.gov
1 2 3 4 5 6 7 8 | m <- MSnID(".")
mzids <- system.file("extdata","phospho.mzid.gz",package="MSnID")
m <- read_mzIDs(m, mzids)
head(m$accessions)
conv_tab <- fetch_conversion_table("Homo sapiens", "UNIPROT", "SYMBOL")
m2 <- remap_accessions(m, conv_tab, "\\|([^|-]+)(-\\d+)?\\|")
head(m2$accessions)
unlink(".Rcache", recursive=TRUE)
|
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