WGCNA (version 1.25-1)

standardScreeningNumericTrait: Standard screening for numeric traits

Description

Standard screening for numeric traits based on Pearson correlation.

Usage

standardScreeningNumericTrait(datExpr, yNumeric, corFnc = cor,
                              corOptions = list(use = 'p'),
                              alternative = c("two.sided", "less", "greater"),
                              qValues = TRUE,
                              areaUnderROC = TRUE)

Arguments

datExpr

data frame containing expression data (or more generally variables to be screened), with rows corresponding to samples and columns to genes (variables)

yNumeric

a numeric vector giving the trait measurements for each sample

corFnc

correlation function. Defaults to Pearson correlation but can also be bicor.

corOptions

list specifying additional arguments to be passed to the correlation function given by corFnc.

alternative

alternative hypothesis for the correlation test

qValues

logical: should q-values be calculated?

areaUnderROC

logical: should are under the receiver-operating curve be calculated?

Value

• Data frame with the following components:
• ID
  Gene (or variable) identifiers copied from colnames(datExpr)
• cor
  correlations of all genes with the trait
• Z
  Fisher Z statistics corresponding to the correlations
• pvalueStudent
  Student p-values of the correlations
• qvalueStudent
  (if input qValues==TRUE) q-values of the correlations calculated from the p-values
• AreaUnderROC
  (if input areaUnderROC==TRUE) area under the ROC
• nPresentSamples
  number of samples present for the calculation of each association.

Details

The function calculates the correlations, associated p-values, area under the ROC, and q-values

See Also

standardScreeningBinaryTrait, standardScreeningCensoredTime