ModulePreservation: a easy method for Module Preservation in FastWGCNA pipeline

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

If you want to test the preservation of modules created by FastWGCNA and you have also another datasets as validataion cohorts,ModulePreservation would be a nice function for this mission.

Usage

ModulePreservation(object, valid.matrix = list(), nPermutations = 50,
  randomSeed = 1, quickCor = 0, verbose = 3, cutoff.Z = 10,
  report = T, width = 15, height = 7.5, save.path = "WGCNA",
  names = "love")

Arguments

object	a result from FastWGCNA
valid.matrix	a list of expression matrix with genes rows and sample cols.
nPermutations	specifies the number of permutations that will be calculated in the permutation test.
randomSeed	seed for the random number generator. If NULL, the seed will not be set. If non-NULL and the random generator has been initialized prior to the function call, the latter's state is saved and restored upon exit
quickCor	number between 0 and 1 specifying the handling of missing data in calculation of correlation. Zero means exact but potentially slower calculations; one means potentially faster calculations, but with potentially inaccurate results if the proportion of missing data is large. See cor for more details.
verbose	integer level of verbosity. Zero means silent, higher values make the output progressively more and more verbose.
cutoff.Z	Default is 10.10 is efficient enought and should not be changed.
report	whether to do a plot report
save.path	the space of the save file.Default is "WGCNA"
names	part of saved files name
setLabels	the names of expression matrix in valid.matrix.

Details

I.The expression matrix in object would be used as a training cohorts in module preservation evaluation. II.nPermutations = 200 is a usual method but it would be time-consuming.It seems that nPermutations = 50 would be stable enough for module presevation exploration.

Value

LuckyWGCNA object

Author(s)

Weibin Huang<[e-mail]>

See Also

FastWGCNA.

Examples

## This is a simulative process and available only with CORRECT VARIABLES
object = wgcna;rm(wgcna);gc()
valid.matrix = list(Valid1 = rna.fpkm.tumor,
                    Valid2 = rna.fpkm.tumor)
result_MP <- ModulePreservation(object,
                                valid.matrix,
                                nPermutations = 20,
                                cutoff.Z = 10,
                                report = T,
                                width = 15,height = 7.5,
                                save.path = "WGCNA-test",
                                names = "love")

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.