CheckAssay: Check an Input Assay

In gabrielodom/pathwayPCA: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Check an Input Assay

Description

Check the classes, dimensions, missingness, feature variance, feature type, and feature names of a data frame.

Usage

CheckAssay(df, removeNear0 = TRUE, epsilon = 10^-6)

Arguments

df	An assay data frame supplied to the CreateOmics function. The first column is assumed to be the sample IDs, and will be ignored. See CheckSampleIDs for checking sample IDs.
removeNear0	Should columns of df with variance near 0 be removed? Defaults to TRUE.
epsilon	Threshold to consider the variance of a column equal to 0. Defaults to 0.000001.

Details

This function checks that the data frame is not a matrix, that the data frame has more columns than rows (tidy genomic data), that the data frame contains no missing or character values, that no features of the data frame have variance less than epsilon (and removes such features if removeNear0 = TRUE), and checks the data frame for valid column names.

Value

The same data frame, without features with 0 variance, if that data frame passes all checks.

Examples

 # DO NOT CALL THIS FUNCTION DIRECTLY. CALL FROM WITHIN CreateOmics().

## Not run: 
 data("colonSurv_df")
 CheckAssay(colonSurv_df[, -(1:3)])

## End(Not run)

gabrielodom/pathwayPCA documentation built on July 10, 2023, 3:32 a.m.