Quality Control report for expression data

Share:

Description

Generate a report with the exploratory plots for count data that can be generated from the biological information provided. This report is designed to compare two samples or two experimental conditions.

Usage

1
QCreport(input, file = NULL, samples = NULL, factor = NULL, norm = FALSE)

Arguments

input

Object of eSet class coming from readData function or other R packages such as DESeq.

file

String indicating the name of the PDF file that will contain the report. It should be in this format: "filename.pdf". The default name is like this: "QCreport_2013Sep26_15:58:16.pdf".

samples

Vector with the two samples to be compared in the report when "factor" is NULL. If "factor" is not NULL and has more than two levels, samples has to indicate the two conditions to be compared. It can be numeric or character (when names of samples or conditions are provided).

factor

If NULL, individual samples indicated in "samples" are compared. Otherwise, it should be a string indicating the factor containing the experimental conditions to be compared in the report.

norm

TRUE to indicate that data are already normalized.

Value

A pdf file.

Author(s)

Sonia Tarazona

References

Marioni, J.C. and Mason, C.E. and Mane, S.M. and Stephens, M. and Gilad, Y. (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research, 18: 1509–1517.

Examples

1
2
3
4
5
## Load the input object from Marioni's data as returned by readData()
data(myCounts)

## Generate the report
QCreport(mydata, samples = NULL, factor = "Tissue")