findChersOnSmoothed {Ringo} | R Documentation |
Given an ExpressionSet of smoothed probe intensities, an environment with the mapping of probes to chromosomes, and a vector of thresholds for calling genomic sites enriched, this function finds the 'chers' (ChIP-enriched regions) consisting of enriched genomic positions, with probes mapped to them. 'Adjacent' enriched positions are condensed into a single Cher.
findChersOnSmoothed(smoothedX, probeAnno, thresholds, allChr = c(1:19, "X", "Y"), distCutOff = 600, minProbesInRow = 3, cellType = NULL, checkUnique = TRUE, uniqueCodes = c(0), verbose = TRUE)
smoothedX |
Object of class ExpressionSet holding the
smoothed probe intensities, e.g. the result of function
computeRunningMedians . |
probeAnno |
environment containing the probe to genome mapping |
thresholds |
numeric vector of threshold above which smoothed
probe intensities are considered to correspond to enriched
probes. The vector has to be of length equal the number of samples
in smoothedX , with a single threshold for each sample. |
allChr |
character vector of all chromosomes, on which Chers are
to be found. Every chromosome here has to have probes mapped to it
in the probeAnno environment. |
distCutOff |
integer; maximum amount of base pairs at which enriched probes are condensed into one Cher. |
minProbesInRow |
integer; minimum number of enriched
probes required for a Cher; see details for further
explanation. |
cellType |
character; name of cell type the data comes from, is
either a. of length one indicating the column of
pData(smoothedX) that holds the cell type OR b. of length one
indicating the common cell type for all samples in the
ExpressionSet OR c. of length equal to ncol(smoothedX)
specifying the cell type of each sample individually. |
checkUnique |
logical; indicates whether the uniqueness indicator of probe matches from the probeAnno environment should be used. |
uniqueCodes |
numeric; which numeric codes in the chromosome-wise match-uniqueness elements of the probeAnno environment indicate uniqueness? |
verbose |
logical; extended output to STDOUT? |
Specifying a minimum number of probes for a Cher (argument
minProbesInRow
) guarantees that a Cher is supported by a
reasonable number of measurements in probe-sparse regions.
For example, if there's only one enriched probe within a certain
genomic 1kb region and no other probes can been mapped to that
region, this single probe does arguably not provide enough evidence
for calling this genomic region enriched.
A list of class cherList
, holding objects of class cher
that were found on the supplied data.
Joern Toedling toedling@ebi.ac.uk
cherByThreshold
,computeRunningMedians
,
relateChers
exDir <- system.file("exData",package="Ringo") load(file.path(exDir,"exampleProbeAnno.rda")) load(file.path(exDir,"exampleX.rda")) smoothX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno, modColumn = "Cy5", allChr = "9", winHalfSize = 400) chersX <- findChersOnSmoothed(smoothX, probeAnno=exProbeAnno, thresholds=0.45, allChr="9", distCutOff=600, cellType="human") if (interactive()) plot(chersX[[1]], smoothX, probeAnno=exProbeAnno, gff=exGFF) chersX <- relateChers(chersX, exGFF) as.data.frame.cherList(chersX)