parse_fasta: Parses FASTA for accession lookups

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Parses FASTA for accession lookups

Description

NA genes are replaced with prot_acc

Usage

parse_fasta(df, fasta, entrez, warns = TRUE)

Arguments

df	An input data frame.
fasta	Character string(s) to the name(s) of fasta file(s) with prepended directory path. The fasta database(s) need to match those used in MS/MS ion search. There is no default and users need to provide the correct file path(s) and name(s).
entrez	Character string(s) to the name(s) of entrez file(s) with prepended directory path. At the NULL default, a convenience lookup is available for species among c("human", "mouse", "rat"). For other species, users need to provide the file path(s) and name(s) for the lookup table(s). See also Uni2Entrez and Ref2Entrez for preparing custom entrez files.
warns	Logical; if TRUE, show warning message(s).

Value

A lookup table, acc_lookup.

See Also

read_fasta for the definition of fasta_name(s).

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.