estimateFragmentCenters {MMDiff2} | R Documentation |
This function computes average shifts between forward and reverse strand and applies it to estimate fragment centers.
estimateFragmentCenters(MD, shift = NULL, draw.on = FALSE)
MD |
DBAmmd Object. This Object can be created using |
shift |
can be set if the offset between forward and reverse strand is known (e.g. 1/2 median fragment size). In this case shift will not be estimated (DEFAULT: NULL) |
draw.on |
plot scatterplots for counts on forward vs reverse strand and histograms of determined shifts (DEFAULT: FALSE) |
DBAmmd object with updated slots Reads
and MetaData
.
DBAmmd
, getPeakReads
,
compHists
## Example using a small data set provided with this package data("MMD") MMD.1 <- estimateFragmentCenters(MMD) # To access centers of fragments: Reads.C <- Reads(MMD.1,'Center') # To access the determined shifts for each sample: meta <- metaData(MMD.1) meta$AnaData$Shifts