mycobacrvR (version 1.1)

filter.firstlayer: Filter first layer data

Description

filter.firstlayer is a function to filter first layer data

Usage

filter.firstlayer(data, organism, ginumber, spaanscore, 
subcelllocal, tmhelices, Hrefhits)

Arguments

data

A character string specifying filenamme containing first layer data table

organism

A character vector specifying species name present in "organism.txt"

ginumber

A numeric vector specifying ginumber

spaanscore

A numeric vector specifying SPAAN score threshold

subcelllocal

A character vector specifying location of the protein

tmhelices

A numeric vectr specifying number of TM helix

Hrefhits

A character vector specifying non similarity to Human Reference Proteins

Value

A file of filtered proteins named "filtered_firstlayer.txt" using the given arguments

Details

This function filters the first layer data according to "motif and topology", "subcellular location" and "homology". Input data (firstlayer.txt) for this function is present in "/data_mycobacrvR/" directory, therefore set working directory to "~/data_mycobacrvR/" before using this function. Defalult value for ginumber,spaanscore,subcelllocal,tmhelices and Hrefhits is "ALL", >0.6, "Extracellular OR Cellwall", <2 and "No Hits found"

Examples

# NOT RUN {
filter.firstlayer("firstlayer.txt",organism="Mycobacterium avium 104")
# }