qualityReport {tilingArray} | R Documentation |
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.
qualityReport(x, hybeType, normRef = NULL, compress = TRUE, selectGenes, gff, probeAnno, output = "HTML", outputDir = ".", verbose = TRUE)
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? |
This function is called for producing quality reports in a specified format and does not return anything.
Wolfgang Huber