RVA (version 0.0.5)

validate.annot: Validate Annotation Table

Description

Ensure that an annotation has all of the required columns.

Usage

validate.annot(
  data,
  annot,
  annot.flags,
  sample.id,
  fill = "CPM",
  baseline.flag = NULL,
  baseline.val = NULL
)

Arguments

data

The input count data.

annot

The annotation dataframe.

annot.flags

The vector of annotation flags passed by the user.

sample.id

Sample id label to check if in annot.

fill

The fill value indicated by the user,"count" or "CPM".

baseline.flag

The baseline.flag passed by the user.

baseline.val

The baseline value passed by the user.

Details

The function will check the following:

• The annot.flags values are columns in annot

• If fill = "cfb": validate the baseline.flag and baseline.val parameters.

• sample.id is a column in annot.

References

Xingpeng Li, Tatiana Gelaf Romer & Siddhartha Pachhai RVA - RNAseq Visualization Automation tool.