filter.firstlayer {mycobacrvR}

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

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"

Value

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

Author(s)

Deepika Kulshreshtha, Rupanjali Chaudhuri, S. Ramachandran

Examples

## Not run: filter.firstlayer("firstlayer.txt",organism="Mycobacterium avium 104")