parseInputFile: Parse files of gene names and group identifiers to create...

In biscuit13161/UNGeneAnno: Collate Gene Annotation Data from Uniprot and NIH Gene Databases

Description

parseInputFile takes a mixed file containing group identifiers (numeric) and gene names, returning the list of group identifiers and genes with the remaining columns removed. The package was originally written to work from a file laid out thus: group_id1 gene_name1 gene_name2 group_id2 gene_name1 gene_name3 The methods assume that both group identifiers and gene names are alphanumeric; the group identifiers, where present, begining with a number and gene names starting with a character. please note, this populates the vector with only the alphanumric strings beginning each line of the input file. Also, RNA genes (begining ENSG000) are currently excluded.

Usage

parseInputFile(x, file)

## S4 method for signature 'geneanno'
parseInputFile(x, file)

Arguments

x	object of class geneanno.
file	character string providing the name of the input file

Value

vector of character strings, as exemplified by the inputlist data object.

Methods (by class)

• geneanno: vector of character strings

Examples

data("inputlist")
write(myinputlist,file="inputlist.txt")
x <- geneanno()
x <- parseInputFile(x,"inputlist.txt")

biscuit13161/UNGeneAnno documentation built on May 26, 2019, 2:33 a.m.