Usage
coocnet(dataFile = "", dataType = "DNA", conservativeFilter = 0.95, cooccurFilter = NULL, networkFile = "cooccurNetwork", module = FALSE, moduleFile = "cooccurNetworkModule", property = FALSE, propertyFile = "cooccurNetworkProperty", siteCo = FALSE, siteCoFile = "siteCooccurr", sampleTimes = 100, debug = FALSE)
Arguments
dataFile
file name with full path of DNA, protein, SNP data or other kinds of data
dataType
the type of data. It could be 'DNA' (default), 'protein', 'SNP' or 'other'
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;
cooccurFilter
a number in the range of 0~1. It determines whether two columns are perfect co-occurrence;
networkFile
file name with full path for storing the co-occurrence network for each row;
module
FALSE by default. If it is set to be TRUE, the modules in each network of the networkFile would be calculated.
moduleFile
file name with full path for storing the modules for co-occurrence network;
property
FALSE by default. If it is set to be TRUE, the properties for each network of the networkFile, including the network diameter, connectivity, ConnectionEffcient and so on, would be calculated.
propertyFile
character, file name with full path for storing the modules for co-occurrence network;
siteCo
FALSE by default. If it is set to be TRUE, the extent of co-occurrence between all pairs of columns would be calculated. It is defined as the ratio of rows with perfect co-occurrence.
siteCoFile
file name with full path for storing the extent of co-occurrence between all pairs of columns, and the related p-values. The later are calculated by simulations as follows firstly, all columns in the data are randomly permutated; then, the pairwise siteCos are calculated. This process would be repeated N times (the value depends on the parameter sampleTimes). For each pair of columns, the rank of the original siteCo in the N siteCos derived from simulations are considered as the p-value for the original siteCo.
sampleTimes
a integer of permutations in the simulation when calculating the p-values.
debug
FALSE by default; to indicate whether the debug message will be displayed or not