increasedBindingRegions {SimBindProfiles} | R Documentation |
This function is used to classify two Binding Profiles into regions which are more bound in one data set than the other.
increasedBindingRegions(xSet, sgrset = c(1, 2), bound.cutoff, diff.cutoff, probes, probe.max.spacing, writeBedFile = TRUE)
xSet |
object of class ExpressionSet |
sgrset |
vector of lenght 2; specifying which data sets to compare from the ExpressionSet |
bound.cutoff |
numeric; threshold above probes are considered “bound” |
diff.cutoff |
numeric; difference threshold to determine if object 1 and object 2 are uniquely bound |
probes |
integer; minimum number of probes in a valid region |
probe.max.spacing |
integer; maximum number of base pairs in a gap before splitting a region into 2 regions |
writeBedFile |
logical; should a bed file be written |
Probe signal values above the bound.cutoff threshold for both data sets are compared where set 1 is above the diff.cutoff of set 2. These probes are then filtered into regions using the probes and probe.max.spacing details. The score is calculated as mean (probes in region set 1 minus set 2). Optional bed file formated result files are written using the choosen options in the file names.
data.frame with the following columns:
name |
name(s) of data set to which region belongs |
class.group |
class group, in this case only 1 |
chr |
chromsome |
start |
start position of region |
end |
end position of region |
scrore |
score of region |
nProbes |
number of probes in region |
Bettina Fischer, Robert Stojnic
pairwiseRegions
,
compensationRegions
,
threewayRegions
,
plotBoundProbes
dataPath <- system.file("data",package="SimBindProfiles") load(file.path(dataPath,"SGR.RData")) overcompBC <- increasedBindingRegions(SGR, sgrset=c(2,3), bound.cutoff=1.86, diff.cutoff=1.4, probes=10, probe.max.spacing=200)