Description Usage Arguments Details Value See Also Examples
takes a readDepth object containing read counts and uses loess correction to account for GC content bias. Updates the @chrs rd column and adds a "gc" column containing that bin's GC content percentage
1 | rd.gcCorrect(rdo, meth=FALSE, outlierPercentage=0.01)
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rdo |
a readDepth object created with new("rdObject") and filled with read counts using the readDepth() command |
meth |
if this data consists of bisulfite reads and a methylation map is present in annotations/methMap, gc correction will be done while taking into account the bisulfite treatment that converts C -> U and methylated bases that were protected from this conversion |
outlierPercentage |
Removes the highest and lowest N This prevents overfitting near the extremes, which loess is susceptible to. Default value is 0.01 |
Assumes that files containing gc content and unmappable regions are in place (see full readDepth documentation for proper directory structure).
returns a rd object with the read depth values altered to reflect gc content composition-induced bias.
'readDepth'
1 2 3 4 5 6 7 8 9 10 11 | ##create a rdObject, set bin params
# x <- new("rdObject")
##fill the bins with reads
# x.reads <- readDepth(x)
##do gc correction on the read counts
# x.map <- rd.mapCorrect(x.reads)
##do gc correction on the read counts
# x.gcCorr = rd.gcCorrect(x.map)
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