WGCNA (version 1.13)

standardScreeningNumericTrait: Standard screening for numeric traits

Description

Standard screening for numeric traits based on Pearson correlation.

Usage

standardScreeningNumericTrait(datExpr, yNumeric,
                              corFnc = "cor", corOptions = "use = 'p'", qValues = 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

character string specifying the function to be used to calculate co-expression similarity for correlation networks. Defaults to Pearson correlation. Any function returning values between -1 and 1 can be used.

corOptions

character string specifying additional arguments to be passed to the function given by corFnc. Use "use = 'p', method = 'spearman'" to obtain Spearman correlation.

qValues

logical: should q-values be calculated?

Value

• List with the following components:
• ID
  Gene (or variable) identifiers copied from colnames(datExpr)
• cor
  correlations of all genes with the trait
• pvalueStudent
  Student p-values of the correlations
• qvalueStudent
  (if input qValues==TRUE) q-values of the correlations calculated from the p-values
• AreaUnderROC
  area under the ROC

Details

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

See Also

standardScreeningBinaryTrait, standardScreeningCensoredTime