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* add merge of external counts functionality * add the citation to nature communications * fix rd man page linking * fix minor warnings in BiocCheck/RCheck * fix/catch biomaRt specific issues
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,163 @@ | ||
| #' | ||
| #' Merge external data | ||
| #' | ||
| #' To boost its own sequencing data, one can download existing and precounted | ||
| #' data. This function merges the existing \code{FraserDataSet} with | ||
| #' external count data. | ||
| #' | ||
| #' For more details on existing datasets have a look at: | ||
| #' <https://github.com/gagneurlab/drop#datasets> | ||
| #' | ||
| #' Since FRASER can not hand NA values, the merge will return only the | ||
| #' intersecting regions and will drop any non overlapping features. This has to | ||
| #' be kept in mind when analysing rare disease samples. | ||
| #' | ||
| #' @param fds A \code{FraserDataSet} | ||
| #' @param countFiles A character vector of file names pointing to the external | ||
| #' count data. The vector has to be names or the files have to start | ||
| #' with \code{k_j}, \code{k_theta}, \code{n_psi3}, \code{n_psi5}, | ||
| #' \code{n_theta}. | ||
| #' @param sampleIDs The samples to be merged from the external data. | ||
| #' @param annotation A sample annotation of the external data (optional). | ||
| #' | ||
| #' @return Merged \code{FraserDataSet} object. | ||
| #' | ||
| #' @examples | ||
| #' anno <- fread(system.file("extdata", "externalCounts", | ||
| #' "annotation.tsv.gz", package="FRASER")) | ||
| #' ctsFiles <- list.files(full.names = TRUE, pattern="counts", | ||
| #' system.file("extdata", "externalCounts", package="FRASER")) | ||
| #' | ||
| #' fds <- createTestFraserDataSet() | ||
| #' fds_merged <- mergeExternalData(fds, ctsFiles, anno[,sampleID], anno) | ||
| #' | ||
| #' K(fds, "psi5") | ||
| #' K(fds_merged, "psi5") | ||
| #' | ||
| #' @export | ||
| mergeExternalData <- function(fds, countFiles, sampleIDs, annotation=NULL){ | ||
|
|
||
| # check input | ||
| checkFraserDataSet(fds) | ||
| checkCountData(fds) | ||
|
|
||
| if(length(countFiles) != 5){ | ||
| stop("You have to provide 5 files, but only ", length(countFiles), | ||
| " were provided.") | ||
| } | ||
| if(is.null(names(countFiles))){ | ||
| names(countFiles) <- gsub("(_counts)?.tsv.gz", "", basename(countFiles)) | ||
| } | ||
| reqNames <- c("k_j", "k_theta", "n_psi3", "n_psi5", "n_theta") | ||
| if(any(!reqNames %in% unique(names(countFiles)))){ | ||
| stop("Please name the input or the files correctly. We are missing: ", | ||
| paste(collapse=", ", | ||
| reqNames[!reqNames %in% names(countFiles)])) | ||
| } | ||
| if(any(!file.exists(countFiles))){ | ||
| stop("Provided files are missing! We are missing: ", | ||
| paste(collapse=", ", countFiles[!file.exists(countFiles)])) | ||
| } | ||
| if(any(unique(sampleIDs) != sampleIDs)){ | ||
| stop("Provided sampleIDs have to be unique!") | ||
| } | ||
| sampleIDs <- as.character(sampleIDs) | ||
|
|
||
| # load external counts | ||
| message("Loading provided counts") | ||
| names(reqNames) <- reqNames | ||
| extCts <- lapply(reqNames, function(id){ | ||
| gr <- makeGRangesFromDataFrame(fread(countFiles[id]), | ||
| keep.extra.columns=TRUE) | ||
| if(any(!sampleIDs %in% colnames(mcols(gr)))){ | ||
| stop("Can not find provided sampleID in count data. Missing IDs: ", | ||
| paste(collapse=", ", | ||
| sampleIDs[!sampleIDs %in% colnames(mcols(gr))])) | ||
| } | ||
| gr[,sampleIDs] | ||
| }) | ||
| stopifnot(all(granges(extCts[['k_j']]) == granges(extCts[['n_psi3']]))) | ||
| stopifnot(all(granges(extCts[['k_j']]) == granges(extCts[['n_psi5']]))) | ||
| stopifnot(all(granges(extCts[['k_theta']]) == granges(extCts[['n_theta']]))) | ||
|
|
||
| # | ||
| # merging colData | ||
| # | ||
| message(date(), ": Merging data ...") | ||
| if(!is.null(annotation)){ | ||
| annotation <- DataFrame(annotation) | ||
| } else { | ||
| annotation <- DataFrame(sampleID=as.character(sampleIDs)) | ||
| } | ||
| rownames(annotation) <- annotation[,"sampleID"] | ||
| newColData <- DataFrame(rbind(fill=TRUE, | ||
| as.data.table(colData(fds)), | ||
| as.data.table(annotation[sampleIDs,]))) | ||
| rownames(newColData) <- newColData[,"sampleID"] | ||
|
|
||
| # | ||
| # merge psi5/psi3 data | ||
| # | ||
| extractExtData <- function(fds, countFun, type, ov, extData, extName){ | ||
| ans <- as.matrix(cbind(countFun(fds, type=type)[from(ov),], | ||
| mcols(extData[[extName]])[to(ov),])) | ||
| mode(ans) <- "integer" | ||
| ans | ||
| } | ||
|
|
||
| # find overlap | ||
| if(all(strand(rowRanges(fds, type="j")) == "*")){ | ||
| for(id in reqNames){ | ||
| strand(extCts[[id]]) <- "*" | ||
| } | ||
| } | ||
| ov <- findOverlaps(rowRanges(fds, type="j"), extCts[['k_j']], type="equal") | ||
|
|
||
| newCtsK_J <- extractExtData(fds, K, "j", ov, extCts, "k_j") | ||
| newCtsN_psi5 <- extractExtData(fds, N, "psi5", ov, extCts, "n_psi5") | ||
| newCtsN_psi3 <- extractExtData(fds, N, "psi3", ov, extCts, "n_psi3") | ||
|
|
||
|
|
||
| # | ||
| # merge theta data | ||
| # | ||
| # find overlap | ||
| ovss <- findOverlaps(rowRanges(fds, type="theta"), | ||
| extCts[['k_theta']], type="equal") | ||
|
|
||
| newCtsK_theta <- extractExtData(fds, K, "theta", ovss, extCts, "k_theta") | ||
| newCtsN_theta <- extractExtData(fds, N, "theta", ovss, extCts, "n_theta") | ||
|
|
||
|
|
||
| # | ||
| # finalize merged FraserDataObject | ||
| # | ||
| nsr <- SummarizedExperiment( | ||
| colData=newColData, | ||
| assays=SimpleList( | ||
| rawCountsSS=newCtsK_theta, | ||
| rawOtherCounts_theta=newCtsN_theta - newCtsK_theta), | ||
| rowRanges=rowRanges(fds, type="theta")[ | ||
| from(ovss),c("spliceSiteID", "type")]) | ||
|
|
||
| ans <- new("FraserDataSet", | ||
| name = name(fds), | ||
| bamParam = scanBamParam(fds), | ||
| strandSpecific = strandSpecific(fds), | ||
| workingDir = workingDir(fds), | ||
| colData = newColData, | ||
| assays=Assays(SimpleList( | ||
| rawCountsJ=newCtsK_J, | ||
| rawOtherCounts_psi5=newCtsN_psi5 - newCtsK_J, | ||
| rawOtherCounts_psi3=newCtsN_psi3 - newCtsK_J)), | ||
| nonSplicedReads = nsr, | ||
| rowRanges = rowRanges(fds)[from(ov),c("startID", "endID")], | ||
| elementMetadata = DataFrame(newCtsK_J[,integer(0)])) | ||
|
|
||
| # | ||
| # compute new psi values | ||
| # | ||
| ans <- calculatePSIValues(ans) | ||
|
|
||
| ans | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,24 +1,24 @@ | ||
| citHeader("To cite FRASER in publications please use:") | ||
| citEntry(entry = "article", | ||
| title = "Detection of aberrant splicing events in RNA-seq data with FRASER", | ||
| title = "Detection of aberrant splicing events in RNA-seq data using FRASER", | ||
| author = personList( | ||
| person("Christian", "Mertes"), | ||
| person("Ines", "Scheller"), | ||
| person(c("Ines", "F"), "Scheller"), | ||
| person(c("Vicente", "A"), "Y\\'{e}pez"), | ||
| person(c("Muhammed", "H"), "\\c{C}elik"), | ||
| person("Yingjiqiong", "Liang"), | ||
| person(c("Laura", "S"), "Kremer"), | ||
| person("Mirjana", "Gusic"), | ||
| person("Holger", "Prokisch"), | ||
| person("Julien", "Gagneur")), | ||
| journal = "biorxiv", | ||
| volume = "", | ||
| number = "", | ||
| pages = "", | ||
| year = "2019", | ||
| issn = "", | ||
| doi = "10.1101/2019.12.18.866830", | ||
| journal = "Nature Communications", | ||
| volume = "12", | ||
| issue = "1", | ||
| pages = "529", | ||
| year = "2021", | ||
| issn = "2041-1723", | ||
| doi = "10.1038/s41467-020-20573-7", | ||
| textVersion = paste( | ||
| "Mertes C, Scheller I et al.,", | ||
| "Detection of aberrant splicing events in RNA-seq data with FRASER.", | ||
| "biorxiv, 2019, 10.1101/2019.12.18.866830.") ) | ||
| "Mertes, C., Scheller, I.F., Yepez, V.A. et al.", | ||
| "Detection of aberrant splicing events in RNA-seq data using FRASER.", | ||
| "Nat Commun 12, 529 2021. https://doi.org/10.1038/s41467-020-20573-7.") ) |
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