Nothing
R/accessor-methods.R
In ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control
Defines functions
.callRatio
.checkPercentages
.summaryDatasetList
## Methods to access slots
setMethod(
f = "getBam",
signature = "Experiment",
definition = function(theObject){
return(theObject@endogenousBam)
})
setMethod(
f = "getBam",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getBam",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@inputBam)
})
setMethod(
f = "getBam",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getBam",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getExogenousBam",
signature = "Experiment",
definition = function(theObject){
return(theObject@exogenousBam)
})
setMethod(
f = "getBigWigFile",
signature = "Experiment",
definition = function(theObject){
return(theObject@bigWigFile)
})
setMethod(
f = "getBigWigFile",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getBigWigFile",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@inputBigWig)
})
setMethod(
f = "getBigWigFile",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getBigWigFile",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getBigWigFile",
signature = "ChIPSeqSpikeDatasetList",
definition = function(theObject){
bigwig_vec <- unlist(lapply(theObject@datasetList,
function(dataset){
bw_vec <- getBigWigFile(dataset)
bw_vec <- c(bw_vec, unlist(
lapply(dataset@experimentList,
function(exp){
return(getBigWigFile(exp))
}
)))
return(bw_vec)
}))
return(bigwig_vec)
})
setMethod(
f = "getExperimentListBigWigs",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
bigWigFiles_vec <- unlist(lapply(theObject@experimentList,
function(x){return(getBigWigFile(x))}))
return(bigWigFiles_vec)
})
setMethod(
f = "getExperimentListBigWigs",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
bigWigFiles_vec <- unlist(lapply(theObject@experimentListLoaded,
function(x){return(getBigWigFile(x))}))
return(bigWigFiles_vec)
})
setMethod(
f = "getExpName",
signature = "Experiment",
definition = function(theObject){
return(theObject@expName)
})
setMethod(
f = "getExpName",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
result <- unlist(lapply(theObject@experimentList, function(exp){
return(getExpName(exp))
}))
return(as.character(result))
})
setMethod(
f = "getExpName",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
result <- unlist(lapply(theObject@experimentListLoaded,
function(exp){
return(getExpName(exp))
}))
return(as.character(result))
})
setMethod(
f = "getExpName",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getScalingFactor",
signature = "Experiment",
definition = function(theObject){
return(theObject@endogenousScalingFactor)
})
setMethod(
f = "getScalingFactor",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getScalingFactor",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@inputScalingFactor)
})
setMethod(
f = "getScalingFactor",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getScalingFactor",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getExogenousScalingFactor",
signature = "Experiment",
definition = function(theObject){
return(theObject@exogenousScalingFactor)
})
setMethod(
f = "getExogenousScalingFactor",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getCount",
signature = "Experiment",
definition = function(theObject){
return(theObject@endoCount)
})
setMethod(
f = "getCount",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getCount",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@inputCount)
})
setMethod(
f = "getCount",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getCount",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getExoCount",
signature = "Experiment",
definition = function(theObject){
return(theObject@exoCount)
})
setMethod(
f = "getExoCount",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getAverageBindingValues",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@plotSetArrayList)
})
setMethod(
f = "getAverageBindingValues",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getAverageBindingValues",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getMatBindingValues",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@matBindingValList)
})
setMethod(
f = "getMatBindingValues",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getMatBindingValues",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getLoadedData",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(theObject@inputBigWigLoaded)
})
setMethod(
f = "getLoadedData",
signature = "ExperimentLoaded",
definition = function(theObject){
return(theObject@loadedBigWigFile)
})
setMethod(
f = "getDatasetList",
signature = "ChIPSeqSpikeDatasetList",
definition = function(theObject){
return(theObject@datasetList)
})
setMethod(
f = "getDatasetList",
signature = "ChIPSeqSpikeDatasetListBoost",
definition = function(theObject){
return(theObject@datasetList)
})
setMethod(
f = "getExperimentList",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(theObject@experimentList)
})
setMethod(
f = "getExperimentList",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(theObject@experimentListLoaded)
})
## Summary of counts and scaling factors of Experiment object
setMethod(
f = "spikeSummary",
signature = "Experiment",
definition = function(theObject){
result <- matrix(c(getScalingFactor(theObject),
getExogenousScalingFactor(theObject),
getCount(theObject),
getExoCount(theObject)), nrow=1)
rownames(result) <- getExpName(theObject)
colnames(result) <- c("endoScalFact", "exoScalFact",
"endoCount", "exoCount")
return(result)
})
setMethod(
f = "spikeSummary",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
## Summary of counts and scaling factors of ChIPSeqSpikeDataset
setMethod(
f = "spikeSummary",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
stat_list <- mapply(function(x){
return(spikeSummary(x))
}, theObject@experimentList, SIMPLIFY = FALSE)
input <- c(getScalingFactor(theObject), NA,
getCount(theObject), NA)
return(rbind(do.call(rbind, stat_list), input))
})
## Summary of counts and scaling factors of ChIPSeqSpikeDatasetList and
## ChIPSeqSpikeDatasetListBoost
.summaryDatasetList <- function(theObject){
result <- lapply(theObject@datasetList, function(dataset){
return(spikeSummary(dataset))
})
return(do.call(rbind, result))
}
setMethod(f = "spikeSummary",
signature = "ChIPSeqSpikeDatasetList", .summaryDatasetList)
setMethod(f = "spikeSummary",
signature = "ChIPSeqSpikeDatasetListBoost", .summaryDatasetList)
## Summary of counts and scaling factors of ChIPSeqSpikeDatasetBoost
setMethod(
f = "spikeSummary",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
stat_list <- mapply(function(x){
return(spikeSummary(x))
}, theObject@experimentListLoaded, SIMPLIFY = FALSE)
input <- c(getScalingFactor(theObject), NA,
getCount(theObject), NA)
return(rbind(do.call(rbind, stat_list), input))
})
## Checking the endogenous dna ratio
.checkPercentages <- function(ratio_list, names_vec){
invisible(mapply(function(ratio, expname){
if(ratio < 2)
warning(expname,
" contains less than 2% of endogenous dna:",
" The scaling might not work.",
immediate. = TRUE)
if(ratio > 25)
warning(expname, " contains more than ",
"25% of endogenous DNA.", immediate. = TRUE)
}, ratio_list, names_vec))
}
setMethod(
f = "getRatio",
signature = "Experiment",
definition = function(theObject){
total_count <- countBam(getBam(theObject), param=ScanBamParam(
scanBamFlag(isPaired= FALSE,
isUnmappedQuery =NA)))$records
exo_count <- getExoCount(theObject)
percent_exo <- round((exo_count*100)/total_count,
digits=1)
return(as.numeric(percent_exo))
})
setMethod(
f = "getRatio",
signature = "ExperimentLoaded",
definition = function(theObject){
callNextMethod(theObject)
})
setMethod(
f = "getRatio",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
ratio_list <- lapply(theObject@experimentList, function(exp){
return(getRatio(exp))
})
names_vec <- names(ratio_list)
.checkPercentages(ratio_list, names_vec)
result <- do.call(rbind, ratio_list)
colnames(result) <- c("Percentage Exo")
return(result)
})
setMethod(
f = "getRatio",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
ratio_list <- lapply(theObject@experimentListLoaded, function(exp){
return(getRatio(exp))
})
names_vec <- names(ratio_list)
.checkPercentages(ratio_list, names_vec)
result <- do.call(rbind, ratio_list)
colnames(result) <- c("Percentage Exo")
return(result)
})
.callRatio <- function(list_object){
ratioResultList <- lapply(list_object, function(dataset){
return(getRatio(dataset))
})
return(do.call(rbind,ratioResultList))
}
setMethod(
f = "getRatio",
signature = "ChIPSeqSpikeDatasetList",
definition = function(theObject){
.callRatio(theObject@datasetList)
})
setMethod(
f = "getRatio",
signature = "ChIPSeqSpikeDatasetListBoost",
definition = function(theObject){
.callRatio(theObject@datasetList)
})
## Export all files for the object obtained in boost mode
setMethod(
f = "exportBigWigs",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject, verbose = TRUE){
if(verbose)
message("Exporting RPM scaled input.")
export(getLoadedData(theObject), con = getBigWigFile(theObject),
format="BigWig")
invisible(lapply(theObject@experimentListLoaded, function(exp){
if(verbose)
message("Writing spiked ", getExpName(exp))
export(getLoadedData(exp), con = getBigWigFile(exp),
format="BigWig")
}))
})
setMethod(
f = "exportBigWigs",
signature = "ChIPSeqSpikeDatasetListBoost",
definition = function(theObject, verbose = TRUE){
invisible(lapply(theObject@datasetList, function(dataset){
exportBigWigs(dataset, verbose)
}))
})
Try the ChIPSeqSpike package in your browser
Any scripts or data that you put into this service are public.
ChIPSeqSpike documentation built on Nov. 8, 2020, 5:29 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions .callRatio .checkPercentages .summaryDatasetList
## Methods to access slots
setMethod(
f = "getBam",
signature = "Experiment",
definition = function(theObject){
return(theObject@endogenousBam)
})
setMethod(
f = "getBam",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getBam",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@inputBam)
})
setMethod(
f = "getBam",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getBam",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getExogenousBam",
signature = "Experiment",
definition = function(theObject){
return(theObject@exogenousBam)
})
setMethod(
f = "getBigWigFile",
signature = "Experiment",
definition = function(theObject){
return(theObject@bigWigFile)
})
setMethod(
f = "getBigWigFile",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getBigWigFile",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@inputBigWig)
})
setMethod(
f = "getBigWigFile",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getBigWigFile",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getBigWigFile",
signature = "ChIPSeqSpikeDatasetList",
definition = function(theObject){
bigwig_vec <- unlist(lapply(theObject@datasetList,
function(dataset){
bw_vec <- getBigWigFile(dataset)
bw_vec <- c(bw_vec, unlist(
lapply(dataset@experimentList,
function(exp){
return(getBigWigFile(exp))
}
)))
return(bw_vec)
}))
return(bigwig_vec)
})
setMethod(
f = "getExperimentListBigWigs",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
bigWigFiles_vec <- unlist(lapply(theObject@experimentList,
function(x){return(getBigWigFile(x))}))
return(bigWigFiles_vec)
})
setMethod(
f = "getExperimentListBigWigs",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
bigWigFiles_vec <- unlist(lapply(theObject@experimentListLoaded,
function(x){return(getBigWigFile(x))}))
return(bigWigFiles_vec)
})
setMethod(
f = "getExpName",
signature = "Experiment",
definition = function(theObject){
return(theObject@expName)
})
setMethod(
f = "getExpName",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
result <- unlist(lapply(theObject@experimentList, function(exp){
return(getExpName(exp))
}))
return(as.character(result))
})
setMethod(
f = "getExpName",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
result <- unlist(lapply(theObject@experimentListLoaded,
function(exp){
return(getExpName(exp))
}))
return(as.character(result))
})
setMethod(
f = "getExpName",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getScalingFactor",
signature = "Experiment",
definition = function(theObject){
return(theObject@endogenousScalingFactor)
})
setMethod(
f = "getScalingFactor",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getScalingFactor",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@inputScalingFactor)
})
setMethod(
f = "getScalingFactor",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getScalingFactor",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getExogenousScalingFactor",
signature = "Experiment",
definition = function(theObject){
return(theObject@exogenousScalingFactor)
})
setMethod(
f = "getExogenousScalingFactor",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getCount",
signature = "Experiment",
definition = function(theObject){
return(theObject@endoCount)
})
setMethod(
f = "getCount",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getCount",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@inputCount)
})
setMethod(
f = "getCount",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getCount",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getExoCount",
signature = "Experiment",
definition = function(theObject){
return(theObject@exoCount)
})
setMethod(
f = "getExoCount",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getAverageBindingValues",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@plotSetArrayList)
})
setMethod(
f = "getAverageBindingValues",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getAverageBindingValues",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getMatBindingValues",
signature = "ChIPSeqSpikeCore",
definition = function(theObject){
return(theObject@matBindingValList)
})
setMethod(
f = "getMatBindingValues",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getMatBindingValues",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(callNextMethod(theObject))
})
setMethod(
f = "getLoadedData",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(theObject@inputBigWigLoaded)
})
setMethod(
f = "getLoadedData",
signature = "ExperimentLoaded",
definition = function(theObject){
return(theObject@loadedBigWigFile)
})
setMethod(
f = "getDatasetList",
signature = "ChIPSeqSpikeDatasetList",
definition = function(theObject){
return(theObject@datasetList)
})
setMethod(
f = "getDatasetList",
signature = "ChIPSeqSpikeDatasetListBoost",
definition = function(theObject){
return(theObject@datasetList)
})
setMethod(
f = "getExperimentList",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
return(theObject@experimentList)
})
setMethod(
f = "getExperimentList",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
return(theObject@experimentListLoaded)
})
## Summary of counts and scaling factors of Experiment object
setMethod(
f = "spikeSummary",
signature = "Experiment",
definition = function(theObject){
result <- matrix(c(getScalingFactor(theObject),
getExogenousScalingFactor(theObject),
getCount(theObject),
getExoCount(theObject)), nrow=1)
rownames(result) <- getExpName(theObject)
colnames(result) <- c("endoScalFact", "exoScalFact",
"endoCount", "exoCount")
return(result)
})
setMethod(
f = "spikeSummary",
signature = "ExperimentLoaded",
definition = function(theObject){
return(callNextMethod(theObject))
})
## Summary of counts and scaling factors of ChIPSeqSpikeDataset
setMethod(
f = "spikeSummary",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
stat_list <- mapply(function(x){
return(spikeSummary(x))
}, theObject@experimentList, SIMPLIFY = FALSE)
input <- c(getScalingFactor(theObject), NA,
getCount(theObject), NA)
return(rbind(do.call(rbind, stat_list), input))
})
## Summary of counts and scaling factors of ChIPSeqSpikeDatasetList and
## ChIPSeqSpikeDatasetListBoost
.summaryDatasetList <- function(theObject){
result <- lapply(theObject@datasetList, function(dataset){
return(spikeSummary(dataset))
})
return(do.call(rbind, result))
}
setMethod(f = "spikeSummary",
signature = "ChIPSeqSpikeDatasetList", .summaryDatasetList)
setMethod(f = "spikeSummary",
signature = "ChIPSeqSpikeDatasetListBoost", .summaryDatasetList)
## Summary of counts and scaling factors of ChIPSeqSpikeDatasetBoost
setMethod(
f = "spikeSummary",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
stat_list <- mapply(function(x){
return(spikeSummary(x))
}, theObject@experimentListLoaded, SIMPLIFY = FALSE)
input <- c(getScalingFactor(theObject), NA,
getCount(theObject), NA)
return(rbind(do.call(rbind, stat_list), input))
})
## Checking the endogenous dna ratio
.checkPercentages <- function(ratio_list, names_vec){
invisible(mapply(function(ratio, expname){
if(ratio < 2)
warning(expname,
" contains less than 2% of endogenous dna:",
" The scaling might not work.",
immediate. = TRUE)
if(ratio > 25)
warning(expname, " contains more than ",
"25% of endogenous DNA.", immediate. = TRUE)
}, ratio_list, names_vec))
}
setMethod(
f = "getRatio",
signature = "Experiment",
definition = function(theObject){
total_count <- countBam(getBam(theObject), param=ScanBamParam(
scanBamFlag(isPaired= FALSE,
isUnmappedQuery =NA)))$records
exo_count <- getExoCount(theObject)
percent_exo <- round((exo_count*100)/total_count,
digits=1)
return(as.numeric(percent_exo))
})
setMethod(
f = "getRatio",
signature = "ExperimentLoaded",
definition = function(theObject){
callNextMethod(theObject)
})
setMethod(
f = "getRatio",
signature = "ChIPSeqSpikeDataset",
definition = function(theObject){
ratio_list <- lapply(theObject@experimentList, function(exp){
return(getRatio(exp))
})
names_vec <- names(ratio_list)
.checkPercentages(ratio_list, names_vec)
result <- do.call(rbind, ratio_list)
colnames(result) <- c("Percentage Exo")
return(result)
})
setMethod(
f = "getRatio",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject){
ratio_list <- lapply(theObject@experimentListLoaded, function(exp){
return(getRatio(exp))
})
names_vec <- names(ratio_list)
.checkPercentages(ratio_list, names_vec)
result <- do.call(rbind, ratio_list)
colnames(result) <- c("Percentage Exo")
return(result)
})
.callRatio <- function(list_object){
ratioResultList <- lapply(list_object, function(dataset){
return(getRatio(dataset))
})
return(do.call(rbind,ratioResultList))
}
setMethod(
f = "getRatio",
signature = "ChIPSeqSpikeDatasetList",
definition = function(theObject){
.callRatio(theObject@datasetList)
})
setMethod(
f = "getRatio",
signature = "ChIPSeqSpikeDatasetListBoost",
definition = function(theObject){
.callRatio(theObject@datasetList)
})
## Export all files for the object obtained in boost mode
setMethod(
f = "exportBigWigs",
signature = "ChIPSeqSpikeDatasetBoost",
definition = function(theObject, verbose = TRUE){
if(verbose)
message("Exporting RPM scaled input.")
export(getLoadedData(theObject), con = getBigWigFile(theObject),
format="BigWig")
invisible(lapply(theObject@experimentListLoaded, function(exp){
if(verbose)
message("Writing spiked ", getExpName(exp))
export(getLoadedData(exp), con = getBigWigFile(exp),
format="BigWig")
}))
})
setMethod(
f = "exportBigWigs",
signature = "ChIPSeqSpikeDatasetListBoost",
definition = function(theObject, verbose = TRUE){
invisible(lapply(theObject@datasetList, function(dataset){
exportBigWigs(dataset, verbose)
}))
})
Try the ChIPSeqSpike package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.