parseInputFile

parseInputFile,geneanno-method

character string providing the name of the input file

file


<code>parseInputFile</code> 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 begining each line of the input file. Also, RNA genes (begining ENSG000) are excluded.


Taking a list of genes, the package collates together the summary
information about those genes from the publicly available resources at Uniprot
and NCBI. Additionally, the package is able to collate publication information
from a search of the NCBI Pubmed database.

I Richard Thompson

ungeneanno

Collate Gene Annotation Data from Uniprot and NIH Gene Databases

parseInputFile function

<ul>
<li> <code>geneanno</code>: vector of character strings
</li>
</ul>

parseInputFile: Parse files of gene names and group identifiers to create unique lists of each

Description

Usage

Arguments

Value

Methods (by class)