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#'@rdname location
#'@aliases location,savProject-method
setMethod("location", signature(project="savProject"), function(project) project@location)
#'@rdname reads
#'@aliases reads,savProject-method
setMethod("reads", signature(project="savProject"), function(project) project@reads)
#'@rdname flowcellLayout
#'@aliases flowcellLayout,savProject-method
setMethod("flowcellLayout", signature(project="savProject"), function(project) project@layout)
#'@rdname run
#'@aliases run,savProject-method
setMethod("run", signature(project="savProject"), function(project) project@runid)
#'@rdname cycles
#'@aliases cycles,savProject-method
setMethod("cycles", signature(project="savProject"), function(project) project@cycles)
#'@rdname directions
#'@aliases directions,savProject-method
setMethod("directions", signature(project="savProject"), function(project) project@directions)
#'@rdname correctedIntensities
#'@aliases correctedIntensities,savProject-method
setMethod("correctedIntensities", signature(project="savProject"), function(project) {
tmp <- project@parsedData[["savCorrectedIntensityFormat"]]@data
if (is.null(tmp)) return(tmp)
return(tmp[,!colnames(tmp) %in% c("x", "y")])
})
#'@rdname qualityMetrics
#'@aliases qualityMetrics,savProject-method
setMethod("qualityMetrics", signature(project="savProject"), function(project) {
tmp <- project@parsedData[["savQualityFormat"]]@data
if (is.null(tmp)) return(tmp)
return(tmp[,!colnames(tmp) %in% c("x", "y")])
})
#'@rdname tileMetrics
#'@aliases tileMetrics,savProject-method
setMethod("tileMetrics", signature(project="savProject"), function(project) {
tmp <- project@parsedData[["savTileFormat"]]@data
return(tmp)
})
#'@rdname extractionMetrics
#'@aliases extractionMetrics,savProject-method
setMethod("extractionMetrics", signature(project="savProject"), function(project) {
tmp <- project@parsedData[["savExtractionFormat"]]@data
if (is.null(tmp)) return(tmp)
return(tmp[,!colnames(tmp) %in% c("x", "y")])
})
#'@rdname errorMetrics
#'@aliases errorMetrics,savProject-method
setMethod("errorMetrics", signature(project="savProject"), function(project) {
tmp <- project@parsedData[["savErrorFormat"]]@data
if (is.null(tmp)) return(tmp)
return(tmp[,!colnames(tmp) %in% c("x", "y")])
})
#'@rdname clusters
#@aliases clusters,savProject,integer
setMethod("clusters", signature(project="savProject", lane="integer"), function(project, lane=1L) {
if (!all(lane %in% 1:flowcellLayout(project)@lanecount)) {
stop(paste("lane" , lane, "is not consistent with number of lanes on flowcell (", flowcellLayout(project)@lanecount, ")", sep=" "))
}
tm <- tileMetrics(project)
return(sum(tm[tm$lane %in% lane & tm$code==102,]$value))
})
#'@rdname pfClusters
#'@aliases pfClusters,savProject,integer
setMethod("pfClusters", signature(project="savProject", lane="integer"), function(project, lane=1L) {
if (!all(lane %in% 1:flowcellLayout(project)@lanecount)) {
stop(paste("lane" , lane, "is not consistent with number of lanes on flowcell (", flowcellLayout(project)@lanecount, ")", sep=" "))
}
tm <- tileMetrics(project)
return(sum(tm[tm$lane %in% lane & tm$code==103,]$value))
})
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