CheckAssay {pathwayPCA} | R Documentation

## 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)

[Package pathwayPCA version 1.2.0 Index]