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 |
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% of reads before loess correction This prevents overfitting near the extremes, to which loess is susceptible. Default value is 0.01 |
resolution |
the resolution at which to bin the values (0.01=1%) |
Assumes that appropriate annotation files are in place (see full copyCat documentation for more information).
returns a rd object with the read depth values altered to reflect gc content composition-induced bias.
'getReadDepth'
1 2 3 4 5 6 7 8 | ##create a rdObject, set bin params
# x <- new("rdObject")
##fill the bins with reads
# x.reads <- getReadDepth(x)
##do gc correction on the read counts
# x.gcCorr = gcCorrect(x)
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