cooccurNet (version 0.1.3)

pprocess: pprocess

Description

Filter the conservative columns (defined as the conservative score greater than the "conservativeFilter")

Usage

pprocess(data=list(),  conservativeFilter=0.95, debug=FALSE)

Arguments

data

a list return from function "readseq()"

conservativeFilter

0.95 by default. a number in the range of 0~1. The column with conservative score greater than it would be filtered in the later analyses;

debug

FALSE by default; to indicate whether the debug message will be displayed or not

Value

a list object containing the original data matrix and frequency matrix

References

Du, X., Wang, Z., Wu, A., Song, L., Cao, Y., Hang, H., & Jiang, T. (2008). Networks of genomic co-occurrence capture characteristics of human influenza A (H3N2) evolution. Genome research, 18(1), 178-187. doi:10.1101/gr.6969007

Examples

data = readseq(dataFile=getexample(dataType="protein"),dataType="protein")
data_process = pprocess(data=data)