filterLoops {diffloop} | R Documentation |
filterLoops
filters out loops that aren't wide, aren't prevalent
within samples or prevalent between samples
filterLoops(dlo, width = 0, nreplicates = 0, nsamples = 1) ## S4 method for signature 'ANY' filterLoops(dlo, width = 0, nreplicates = 0, nsamples = 1)
dlo |
A loops object |
width |
Minimum loop width |
nreplicates |
Minimum number of counts per loop |
nsamples |
Minimum number of samples per loop per counts |
Function that restricts loops in a loops object. width
specifies
the minimum width between anchors. Default is zero. nreplicates
restricts loops to at least this specified amount of counts is present
in at least one sample. Instead of nreplicates
being present in only
one sample, nsamples
specifies how many individual samples that a
loop must have nreplicates
in to be included after filtering.
A loops object
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/') load(rda) # Restrict loops to > 5kb width filtered.jpn1 <- filterLoops(loops.small, 5000, 0, 0) # Restrict loops to > 5kb width and have >= 3 replicates in >= 1 sample filtered.jpn2 <- filterLoops(loops.small, 5000, 3, 1) # Restrict loops to > 10kb width and have >= 3 replicates in >= 2 samples filtered.jpn3 <- filterLoops(loops.small, 10000, 3, 2)