gencooccur: gencooccur

Description

Construct the co-occurrence network

Usage

gencooccur(data = list(), cooccurFilter = NULL, networkFile = "cooccurNetwork", module = FALSE, moduleFile = "cooccurNetworkModule", property = FALSE, propertyFile = "cooccurNetworkProperty", siteCo = FALSE, siteCoFile = "siteCooccurr", sampleTimes = 100, debug = FALSE, parallel = FALSE)

Arguments

data

list, returns from the function "pprocess()"

cooccurFilter

numeric, a number in the range of 0~1. It determines whether two columns are perfect co-occurrence. In default, for the data type of protein, it is set to be 0.9, while for the other data types, it is set to be 1.

networkFile

character, 'cooccurNetwork' be default. It is a file name with full path for storing the co-occurrence network for each row.

module

logic, FALSE by default, to check whether the modules in each network of the networkFile would be calculated.

moduleFile

character, 'cooccurNetworkModule' by default. It is a file name with full path for storing the modules for co-occurrence network.

property

logic, FALSE by default, to check whether the properties for each network of the networkFile, including the network diameter, connectivity, ConnectionEffcient and so on, would be calculated.

propertyFile

character, 'cooccurNetworkProperty' by default. It is a file name with full path storing the properties for each network of the networkFile.

siteCo

logic, FALSE by default, to check whether the residue co-occurence file would be calculated.

siteCoFile

character, 'siteCooccurr' by default. It is a file name with full path for storing the RCOS between all pairs of columns, and the related p-values.

sampleTimes

numeric, an integer of permutations in the simulation when calculating the p-values. It should be greater than 100.

debug

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

parallel

logic, FALSE by default. It only supports Unix/Mac (not Windows) system.

Value

list, all the output file paths are attributed in it. The attribute "networkFile" stores the co-occurrence network for each row; The attribute "moduleFile" is optional. When the module is set to be TRUE, it would be output. It stores the modules for co-occurrence network; The attribute "propertyFile" is optional. When the property is set to be TRUE, it would be output. It stores the properties for co-occurrence network; The attribute "siteCoFile" is optional. When the property is set to be TRUE, it would be output. It stores all the pairwise siteCos between columns.

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

Run this code

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

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