Description Usage Arguments Value References Examples
Construct the co-occurrence network
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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. |
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.
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
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Reading file......
completed. (10,329)
Pre-processing......
Calculating bigram frequency ......
Pre-process......completed. (10,42)
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