cooccurNet (version 0.1.6)

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, memory=NULL)

Arguments

data

list, returns from the function "readseq()".

conservativeFilter

numeric, a number in the range of 0~1, 0.95 by default. It's used to filter the highly conservative columns which the ratio of some residue is larger than the conservationFilter.

debug

logic, FALSE by default, indicates whether the debug message will be displayed or not.

memory

character, the type of matrix, NULL by default. It could be 'memory' or 'sparse'. If it's set to be 'memory', all data would be manipulated in the RAM by using normal matrix and package 'bigmemory'. If it's set to be 'sparse', the package "Matrix" would be used to manipulate massive matrices in memory and initialize huge sparse matrix, which could significantly reduce the RAM consumed. In default, it is set to be NULL, so that the system would determine automatically whether all data is manipulated in the RAM or not, according to the size of data inputted and the RAM available for R.

Value

list, contains the original data matrix, frequency matrix and other informations.

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,conservativeFilter=0.95)