estimateCorrection {QDNAseq} | R Documentation |
Estimate correction to read counts for GC content and mappability.
estimateCorrection(object, span=0.65, family="symmetric", adjustIncompletes=TRUE, maxIter=1, cutoff=4, variables=c("gc", "mappability"), ...)
object |
An |
span |
For |
family |
For |
adjustIncompletes |
A boolean(1) specifying whether |
maxIter |
An integer(1) specifying the maximum number of iterations
to perform, default is 1. If larger, after the first loess fit, bins
with median residuals larger than |
cutoff |
A numeric(1) specifying the number of standard deviations
(as estimated with |
variables |
A character vector specifying which variables to include
in the correction. Can be |
... |
Additional aguments passed to |
Returns a QDNAseqReadCounts
object with the assay data element
fit
added.
Ilari Scheinin
Internally, loess
is used to fit the regression model.
data(LGG150) readCounts <- LGG150 readCountsFiltered <- applyFilters(readCounts) readCountsFiltered <- estimateCorrection(readCountsFiltered)