wgcnatest {DDPNA}

wgcnatest

Description

The major parameter optimization in function blockwiseModules in WGCNA package. The function will do a series of network construction by change various parameter in blockwiseModules and record the result. (it will take a long time)

Usage

wgcnatest(data, power = NULL, maxBlockSize = 5000,
          corType = "pearson", networkType = "unsigned",
          TOMType = "unsigned",detectCutHeight = NULL,
          deepSplit = TRUE, minModSize = TRUE,
          minKMEtoStay = TRUE,minCoreKME = FALSE,
          reassignThreshold = FALSE,mergeCutHeight = FALSE,
          pamRespectsDendro = FALSE,
          maxModNum = 30,minModNum = 8,MaxMod0ratio = 0.3,
          ...)

Arguments

data

protein quantification data used in network construction. Row is sample. Column is protein ID. More information can get from blockwiseModules in WGCNA package.

power

Soft-thresholding power for network construction. The default value is NULL. it will run pickSoftThreshold function in WGCNA package to pick the lowest appropriate power. More information can get from blockwiseModules in WGCNA package.

maxBlockSize

integer giving maximum block size for module detection. More information can get from blockwiseModules in WGCNA package.

corType

one of "pearson" and "bicor". More information can get from blockwiseModules in WGCNA package.

networkType

one of "signed hybrid", "unsigned", "signed". More information can get from blockwiseModules in WGCNA package.

TOMType

one of "none", "unsigned", "signed","signed Nowick", "unsigned 2", "signed 2" and "signed Nowick 2".. More information can get from blockwiseModules in WGCNA package.

detectCutHeight

dendrogram cut height for module detection. The default value is NULL, which means it will calculate the cutheight through correlation r when p value is 0.05. When the value is larger than 0.995, it will set to detectCutHeight or 0.995. More information can get from blockwiseModules in WGCNA package.

deepSplit

The default value is TRUE, which means the function will test deepSplit from 0 to 4. If the value is FALSE, deepSplit is 2. You also can setting integer value between 0 and 4 by yourself. integer value between 0 and 4. More information can get from blockwiseModules in WGCNA package.

minModSize

minimum module size for module detection. The default value is TRUE, which means the function will test 15, 20, 30, 50. If the value is FALSE, minModSize is 20. You also can setting integer value by yourself. More information can get from blockwiseModules in WGCNA package.

minKMEtoStay

The default value is TRUE, which means the function will test 0.1, 0.2, 0.3. If the value is FALSE, minKMEtoStay is 0.3. You also can setting value by yourself. Value between 0 to 1. More information can get from blockwiseModules in WGCNA package.

minCoreKME

The default value is FALSE, minCoreKME is 0.5. If the value is TRUE, which means the function will test 0.4 and 0.5. You also can setting value by yourself. Value between 0 to 1. More information can get from blockwiseModules in WGCNA package.

reassignThreshold

p-value ratio threshold for reassigning genes between modules. The default value is FALSE, reassignThreshold is 1e-6. If the value is TRUE, which means the function will test 0.01 and 0.05. You also can setting value by yourself. More information can get from blockwiseModules in WGCNA package.

mergeCutHeight

dendrogram cut height for module merging. The default value is FALSE, mergeCutHeight is 0.15. If the value is TRUE, which means the function will test 0.15, 0.3 and 0.45. You also can setting value by yourself. More information can get from blockwiseModules in WGCNA package.

pamRespectsDendro

a logical value indicated that whether do pamStage or not. More information can get from blockwiseModules in WGCNA package.

maxModNum

The maximum module number. If network construction make more than maxModnum of modules. The result will not record.

minModNum

The mininum module number. If network construction make less than minModNum of modules. The result will not record.

MaxMod0ratio

The maximum Mod0 protein numbers ratio in total proteins. If network construction make more than MaxMod0ratio in module 0. The result will not record.

...

Other arguments from blockwiseModules in WGCNA packag.

Details

More information can get from blockwiseModules in WGCNA package.

Value

a data.frame contains protein number in each module and the parameter information.

Author(s)

Kefu Liu

Examples

data(imputedData)
wgcnadata <- t(imputedData$intensity)
sft <- SoftThresholdScaleGraph(wgcnadata)
# It will take a lot of time
if (requireNamespace("WGCNA", quietly = TRUE)){
require("WGCNA")
WGCNAadjust <- wgcnatest(wgcnadata, power = sft$powerEstimate)
}