qualityReport {tilingArray}R Documentation

Assess quality of normalized poly-A-RNA samples

Description

Function to analyze quality of (normalized) tiling array data. Provides plots of intensities along the chromosome around specified genes, scatterplots comparing raw and normalized data, and a histogram of z-scores for intensities within annotated coding DNA regions.

Usage

qualityReport(x, hybeType, normRef = NULL, compress = TRUE, selectGenes, 
  gff, probeAnno, output = "HTML", outputDir = ".", verbose = TRUE)

Arguments

x tiling array data, either a character vector, naming the CEL files to analyze, OR an AffyBatch containing the unnormalized data
hybeType character string, naming the type of hybridized data, either 'direct' for directly hybridized RNA (no normalization necessary) or 'reverse' for reverse-transcribed RNA
normRef samples used for normalization of the data, either a character vector naming the CEL-files to use for normalization of x of an AffyBatch containing the expression data of those samples. NULL means 'no normalization'
compress logical; if x and normRef were provided as character vectors, are the related CEL-files compressed?
selectGenes character vector; for which genes are along-chromosome plots to be prepared
gff data frame with genome annotation from the GFF file.
probeAnno environment with probe annotations
output character string, type of output to produce, currently only 'HTML' is supported.
outputDir path to storage directory of quality reports
verbose logical, do you want extended progess output to STDOUT?

Value

This function is called for producing quality reports in a specified format and does not return anything.

Author(s)

Wolfgang Huber

Examples






[Package tilingArray version 1.2.0 Index]