pvalByGeneSet: Apply a test to different genesets using the same...

In pgpmartin/GeneNeighborhood: Analyze the Neighborhood (Upstream/Downstream Neighbors) of Genes

Description

Apply a test to different genesets using the same reference/control set

Usage

pvalByGeneSet(tbdist, univ = "Universe", FUN, ...)

Arguments

tbdist	A data frame with the following columns: Distance. Distance in bp. GeneName. Name of the focus gene. GeneSet. Name of the Gene Set
univ	Character string giving the name of the control set (should be in the GeneSet column).
FUN	A function returning a single pvalue and that takes at least 2 arguments: the data frame .x and .y, of the same form as tbdist, containing the distances for the test set and for the control/reference set. and returns a single p-value.
...	further arguments passed to FUN

Value

A tibble with 2 columns: GeneSet and pvalue

Author(s)

Pascal GP Martin

See Also

replicate colMedians

Examples

## Create some random distance data
  set.seed(123)
  mydistData <- data.frame(GeneName = stringi::stri_rand_strings(600, 5),
                           Distance = sample(1:5000, 600, replace=TRUE),
                           GeneSet = sample(c("TestSet1", "TestSet2", "RefSet"),
                                            600, replace= TRUE))
## Apply Kolmogorov-Smirnov test to the different test sets
  pvalByGeneSet(tbdist = mydistData,
                univ = "RefSet",
                FUN = ksfun)

pgpmartin/GeneNeighborhood documentation built on Sept. 2, 2021, 6:37 a.m.