Usage
coocnet(dataFile = "", dataType = "protein", conservativeFilter = 0.95, cooccurFilter = NULL, networkFile = "cooccurNetwork", module = FALSE, moduleFile = "cooccurNetworkModule", property = FALSE, propertyFile = "cooccurNetworkProperty", siteCo = FALSE, siteCoFile = "siteCooccurr", sampleTimes = 100, debug = FALSE, parallel = FALSE, memory = NULL)
Arguments
dataFile
character, a FASTA data file name with full path.
dataType
character, 'protein' by default, the type of data will be processed. It could be 'DNA', 'RNA', 'protein', 'SNP' or 'other'.
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.
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.
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.