vector of lenght 3; 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 objects 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 bed file be written
Details
Select probes with a signal above the bound.cutoff in data set 1 and 2 and below in set 3,
and for which the average signal of set 1 and set2 is above the diff.cutoff compared
to set 3. These probes are then filtered into regions using the probes and
probe.max.spacing details. The score is calculated as mean (probes in region
average(set 1 and set 2) minus set 3). Optional bed file formated result files
are written using the choosen options in the file names.
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> library(SimBindProfiles)
Loading required package: Ringo
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: RColorBrewer
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SimBindProfiles/compensationRegions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: compensationRegions
> ### Title: Classify two Binding Profiles - Compensation
> ### Aliases: compensationRegions
>
> ### ** Examples
>
> dataPath <- system.file("data",package="SimBindProfiles")
> load(file.path(dataPath,"SGR.RData"))
> transcompABC <- compensationRegions(SGR, sgrset=c(1,2,3), bound.cutoff=1.86,
+ diff.cutoff=1.4, probes=10, probe.max.spacing=200)
Compensation comparison of SoxNDam & SoxN-DDam vs DDam
Filter data into regions...
Writing SoxNDam.SoxN-DDam.vs.DDam.compensation_b1.86d1.4v10g200.bed ,regions = 8 ...
>
>
>
>
>
> dev.off()
null device
1
>