check.pigengene.input {Pigengene}R Documentation

Quality check on the imput

Description

Checks Data and Labels for NA values, row and column names, etc.

Usage

  check.pigengene.input(Data, Labels, na.rm = FALSE, naTolerance=0.05)

Arguments

Data

A matrix or data frame containing the expression data, with genes corresponding to columns and rows corresponding to samples. Rows and columns must be named.

Labels

A (preferably named) vector containing the Labels (condition types) for Data. Names must agree with rows of Data.

na.rm

If TRUE, NAs in the Data will be replaces with the average of the column, however, if the frequency of NAs in the column is too high, the whole column will be removed.

naTolerance

Upper threshold on the fraction of entries per gene that can be missing. Genes with a larger fraction of missing entries are ignored. For genes with smaller fraction of NA entries, the missing values are imputed from their average expression in the other samples. See check.pigengene.input.

Value

A list of:

Data

The checked Data matrix, NA possibly removed and rows are ordered as names of Labels.

Labels

The checked vector of Labels

Author(s)

Habil Zare

See Also

check.nas, one.step.pigengene, Pigengene-package

Examples

     data(aml)
     Labels <- c(rep("AML",nrow(aml)))
     names(Labels) <- rownames(aml)
     c1 <- check.pigengene.input(Data=aml, Labels=Labels,na.rm=TRUE)
     Data <- c1$Data
     Labels <- c1$Labels

[Package Pigengene version 1.19.52 Index]