coinIndep: Test the independence of 2 sets of distances with the coin...

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

Description

Test the independence of 2 sets of distances with the coin package (only returns the p-value)

Usage

coinIndep(.x, .y)

Arguments

.x	A data frame with distances for the gene set of interest.
.y	A data frame with distances for the control/reference gene set.

Value

The p-value of the independence test from the coin package.

DETAILS

Both .x and .y should contain at least the following columns:

• Distance. Distance in bp.

• GeneName. Name of the focus gene.

• GeneSet. Name of the Gene Set

Author(s)

Pascal GP Martin

See Also

independence_test

Examples

## Create some random distance data
  set.seed(123)
  mydistData <- data.frame(GeneName = stringi::stri_rand_strings(400, 5),
                           Distance = sample(1:5000, 400, replace=TRUE),
                           GeneSet = sample(c("TestSet", "RefSet"),
                                            400, replace= TRUE))
## Compute the p-value of the independence test
  coinIndep(.x = mydistData[mydistData$GeneSet == "TestSet",],
            .y = mydistData[mydistData$GeneSet == "RefSet",])
## If .x is empty, the function returns NA
  coinIndep(.x = mydistData[mydistData$GeneSet == "SomeRandomName",],
            .y = mydistData[mydistData$GeneSet == "RefSet",])
## If .y is empty, the function returns an error
## Not run: 
  coinIndep(.x = mydistData[mydistData$GeneSet == "TestSet",],
            .y = mydistData[mydistData$GeneSet == "SomeRandomName",])
        
## End(Not run)

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