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SuiYue-2308
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Rename setIsoreParameters/isoreParameters to setDiscoveryParameters/discoveryParameters for consistency with setRcAssignmentParameters and setEmParameters naming convention.
1 parent 7ef1e7b commit 5add785

6 files changed

Lines changed: 52 additions & 52 deletions

‎R/bambu-extendAnnotations-utilityExtend.R‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -880,7 +880,7 @@ setNDR <- function(extendedAnnotations, NDR = NULL, includeRef = FALSE, prefix =
880880

881881
#' Extend annotations by clusters
882882
#' @noRd
883-
isore.extendAnnotations.clusters <- function(readClassList, annotations, clusters, NDR, isoreParameters, stranded, bpParameters, fusionMode, verbose = FALSE){
883+
isore.extendAnnotations.clusters <- function(readClassList, annotations, clusters, NDR, discoveryParameters, stranded, bpParameters, fusionMode, verbose = FALSE){
884884
message("--- Start extending annotations for clusters ---")
885885
#if clustering is a csv, create a list with the barcodes for each cluster
886886
#csv must have two cols with heading barcode, cluster
@@ -912,21 +912,21 @@ isore.extendAnnotations.clusters <- function(readClassList, annotations, cluster
912912
rowData(rcf.filt)$startSD <- 0
913913
rowData(rcf.filt)$endSD <- 0
914914
rowData(rcf.filt)$readCount.posStrand <- 0
915-
thresholdIndex <- which(rowData(rcf.filt)$readCount>=isoreParameters$min.readCount)
916-
model <- trainBambu(rcf.filt, verbose = verbose, min.readCount = isoreParameters$min.readCount)
915+
thresholdIndex <- which(rowData(rcf.filt)$readCount>=discoveryParameters$min.readCount)
916+
model <- trainBambu(rcf.filt, verbose = verbose, min.readCount = discoveryParameters$min.readCount)
917917
txScore <- getTranscriptScore(rowData(rcf.filt)[thresholdIndex,], model,
918918
defaultModels)
919919
rowData(rcf.filt)$txScore <- rep(NA,nrow(rcf.filt))
920920
rowData(rcf.filt)$txScore[thresholdIndex] <- txScore
921921
#txScores = cbind(txScores, rowData(rcf.filt)$txScore)
922922
rcfs.clusters[[names(clusters)[i]]] <- rcf.filt
923923
annotations.clusters[[names(clusters)[i]]] <- bambu.extendAnnotations(list(rcf.filt), annotations, NDR,
924-
isoreParameters, stranded, bpParameters, fusionMode, verbose)
924+
discoveryParameters, stranded, bpParameters, fusionMode, verbose)
925925
}
926926
if(length(rcfs.clusters)>0){
927927
print("--- Merging all individual clusters ---")
928928
annotations.clusters[["merged"]] <- bambu.extendAnnotations(rcfs.clusters, annotations, NDR,
929-
isoreParameters, stranded, bpParameters, fusionMode, verbose)
929+
discoveryParameters, stranded, bpParameters, fusionMode, verbose)
930930
}
931931

932932
return(annotations.clusters)

‎R/bambu-extendAnnotations.R‎

Lines changed: 15 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -3,14 +3,14 @@
33
#' @inheritParams bambu
44
#' @noRd
55
bambu.extendAnnotations <- function(readClassList, annotations, NDR,
6-
isoreParameters, stranded, bpParameters, fusionMode = FALSE, verbose = FALSE) {
6+
discoveryParameters, stranded, bpParameters, fusionMode = FALSE, verbose = FALSE) {
77
start.ptm_all <- proc.time()
88
combinedTxCandidates <- isore.combineTranscriptCandidates(readClassList,
99
stranded, ## stranded used for unspliced reduce
10-
min.readCount = isoreParameters[["min.readCount"]],
11-
min.readFractionByGene = isoreParameters[["min.readFractionByGene"]],
12-
min.txScore.multiExon = isoreParameters[["min.txScore.multiExon"]],
13-
min.txScore.singleExon = isoreParameters[["min.txScore.singleExon"]],
10+
min.readCount = discoveryParameters[["min.readCount"]],
11+
min.readFractionByGene = discoveryParameters[["min.readFractionByGene"]],
12+
min.txScore.multiExon = discoveryParameters[["min.txScore.multiExon"]],
13+
min.txScore.singleExon = discoveryParameters[["min.txScore.singleExon"]],
1414
bpParameters,
1515
verbose)
1616
end.ptm_all <- proc.time()
@@ -20,21 +20,21 @@ bambu.extendAnnotations <- function(readClassList, annotations, NDR,
2020
annotations <- isore.extendAnnotations(
2121
combinedTranscripts = combinedTxCandidates,
2222
annotationGrangesList = annotations,
23-
remove.subsetTx = isoreParameters[["remove.subsetTx"]],
24-
min.sampleNumber = isoreParameters[["min.sampleNumber"]],
23+
remove.subsetTx = discoveryParameters[["remove.subsetTx"]],
24+
min.sampleNumber = discoveryParameters[["min.sampleNumber"]],
2525
NDR = NDR,
26-
min.exonDistance = isoreParameters[["min.exonDistance"]],
27-
min.exonOverlap = isoreParameters[["min.exonOverlap"]],
26+
min.exonDistance = discoveryParameters[["min.exonDistance"]],
27+
min.exonOverlap = discoveryParameters[["min.exonOverlap"]],
2828
min.primarySecondaryDist =
29-
isoreParameters[['min.primarySecondaryDist']],
29+
discoveryParameters[['min.primarySecondaryDist']],
3030
min.primarySecondaryDistStartEnd =
31-
isoreParameters[['min.primarySecondaryDistStartEnd1']],
31+
discoveryParameters[['min.primarySecondaryDistStartEnd1']],
3232
min.readFractionByEqClass =
33-
isoreParameters[['min.readFractionByEqClass']],
33+
discoveryParameters[['min.readFractionByEqClass']],
3434
fusionMode = fusionMode,
35-
prefix = isoreParameters[["prefix"]],
36-
baselineFDR = isoreParameters[["baselineFDR"]],
37-
defaultModels = isoreParameters[["defaultModels"]],
35+
prefix = discoveryParameters[["prefix"]],
36+
baselineFDR = discoveryParameters[["baselineFDR"]],
37+
defaultModels = discoveryParameters[["defaultModels"]],
3838
verbose = verbose)
3939
end.ptm_all <- proc.time()
4040
if (verbose) message("extend annotations in ",

‎R/bambu-processReads.R‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@
1414
#' @noRd
1515
bambu.processReads <- function(reads, annotations, genomeSequence,
1616
readClass.outputDir=NULL, yieldSize=1000000, bpParameters,
17-
stranded=FALSE, verbose=FALSE, isoreParameters = setIsoreParameters(NULL),
17+
stranded=FALSE, verbose=FALSE, discoveryParameters = setDiscoveryParameters(NULL),
1818
processByChromosome = FALSE, processByBam = TRUE, trackReads = trackReads, fusionMode = fusionMode,
1919
demultiplexed = FALSE, cleanReads = FALSE, dedupUMI = FALSE, sampleNames = NULL, barcodesToFilter = NULL) {
2020
genomeSequence <- checkInputSequence(genomeSequence)
@@ -48,11 +48,11 @@ bambu.processReads <- function(reads, annotations, genomeSequence,
4848
names(reads)[seq_along(sampleNames)] <- sampleNames
4949
}
5050
}
51-
min.readCount <- isoreParameters[["min.readCount"]]
52-
fitReadClassModel <- isoreParameters[["fitReadClassModel"]]
53-
defaultModels <- isoreParameters[["defaultModels"]]
54-
returnModel <- isoreParameters[["returnModel"]]
55-
min.exonOverlap <- isoreParameters[["min.exonOverlap"]]
51+
min.readCount <- discoveryParameters[["min.readCount"]]
52+
fitReadClassModel <- discoveryParameters[["fitReadClassModel"]]
53+
defaultModels <- discoveryParameters[["defaultModels"]]
54+
returnModel <- discoveryParameters[["returnModel"]]
55+
min.exonOverlap <- discoveryParameters[["min.exonOverlap"]]
5656

5757
if(processByBam){
5858
readClassList <- bplapply(seq_along(reads), function(i) {

‎R/bambu-quantify.R‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,9 +2,9 @@
22
#' @inheritParams bambu
33
#' @import data.table
44
#' @noRd
5-
bambu.quantify <- function(readClassDt, countMatrix, incompatibleCountMatrix, txid.index, GENEIDs, emParameters,
5+
bambu.quantify <- function(readClassDt, countMatrix, incompatibleCountMatrix, txid.index, GENEIDs, emParameters,
66
trackReads = FALSE, returnDistTable = FALSE,
7-
verbose = FALSE, isoreParameters = setIsoreParameters(NULL)) {
7+
verbose = FALSE) {
88
start.ptm <- proc.time()
99
readClassDt$nobs = countMatrix[readClassDt$eqClass.match]
1010
readClassDt$nobs[is.na(readClassDt$nobs)] = 0

‎R/bambu.R‎

Lines changed: 15 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -191,11 +191,11 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
191191
genomeSequence = genome, discovery = discovery,
192192
sampleNames = sampleNames, sampleData = sampleData, quantData = quantData)
193193
}
194-
isoreParameters <- setIsoreParameters(isoreParameters = opt.discovery)
194+
opt.discovery <- setDiscoveryParameters(discoveryParameters = opt.discovery)
195195
#below line is to be compatible with earlier version of running bambu
196-
if(!is.null(isoreParameters$max.txNDR)) NDR = isoreParameters$max.txNDR
197-
rcAssignmentParameters <- setRcAssignmentParameters(rcAssignmentParameters = opt.rcAssignment)
198-
emParameters <- setEmParameters(emParameters = opt.em)
196+
if(!is.null(opt.discovery$max.txNDR)) NDR = opt.discovery$max.txNDR
197+
opt.rcAssignment <- setRcAssignmentParameters(rcAssignmentParameters = opt.rcAssignment)
198+
opt.em <- setEmParameters(emParameters = opt.em)
199199
bpParameters <- setBiocParallelParameters(reads, ncore, verbose, demultiplexed)
200200
xgb.set.config(nthread = 1)
201201
# only when reads is not NULL, this proceed, otherwise, it will jump to quant step
@@ -221,7 +221,7 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
221221
genomeSequence = genome,
222222
readClass.outputDir = rcOutDir, yieldSize = yieldSize,
223223
bpParameters = bpParameters, stranded = stranded, verbose = verbose,
224-
isoreParameters = isoreParameters, trackReads = trackReads,
224+
discoveryParameters = opt.discovery, trackReads = trackReads,
225225
fusionMode = fusionMode,
226226
processByChromosome = processByChromosome, processByBam = processByBam,
227227
demultiplexed = demultiplexed,
@@ -234,14 +234,14 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
234234
if (discovery) {
235235
message("--- Start extending annotations ---")
236236
extendedAnnotations <- bambu.extendAnnotations(readClassList, annotations, NDR,
237-
isoreParameters, stranded, bpParameters, fusionMode, verbose)
237+
opt.discovery, stranded, bpParameters, fusionMode, verbose)
238238
metadata(extendedAnnotations)$warnings = warnings
239239

240240
#### cluster based transcript discovery
241241
if(!is.null(clusters)){
242242
annotations.clusters <- isore.extendAnnotations.clusters(readClassList,
243-
annotations, clusters, NDR,
244-
isoreParameters, stranded, bpParameters, fusionMode, verbose = FALSE)
243+
annotations, clusters, NDR,
244+
opt.discovery, stranded, bpParameters, fusionMode, verbose = FALSE)
245245
metadata(extendedAnnotations)$clusters <- annotations.clusters
246246
}
247247
annotations <- extendedAnnotations
@@ -254,7 +254,7 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
254254
assignReadClasstoTranscripts(
255255
readClassList = readClassList[[i]],
256256
annotations = annotations,
257-
rcAssignmentParameters = rcAssignmentParameters,
257+
rcAssignmentParameters = opt.rcAssignment,
258258
verbose = verbose,
259259
# for bulk data, there is one sampleData (keep sampleData[1]), for single-cell, there is one per sample
260260
sampleMetadata = if(length(sampleData) == 1) sampleData[1] else sampleData[i],
@@ -270,10 +270,10 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
270270
if (quant) {
271271
message("--- Start isoform EM quantification ---")
272272
if(!is.null(NDR) & !discovery)# this step is used when reset NDR is needed
273-
annotations <- setNDR(annotations, NDR,
274-
prefix = isoreParameters$prefix,
275-
baselineFDR = isoreParameters[["baselineFDR"]],
276-
defaultModels2 = isoreParameters[["defaultModels"]])
273+
annotations <- setNDR(annotations, NDR,
274+
prefix = opt.discovery$prefix,
275+
baselineFDR = opt.discovery[["baselineFDR"]],
276+
defaultModels2 = opt.discovery[["defaultModels"]])
277277
if(length(annotations)==0) stop("No valid annotations, if running
278278
de novo please try less stringent parameters")
279279
if(is.null(quantData)) stop("quantData must be provided or assignDist = TRUE")
@@ -318,8 +318,8 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
318318
}
319319
return(bambu.quantify(readClassDt = metadata(quantData_i)$readClassDt, countMatrix = countMatrix,
320320
incompatibleCountMatrix = data.table(GENEID.i = as.numeric(rownames(metadata(quantData_i)$incompatibleCountMatrix)), counts = incompatibleCountMatrix),
321-
txid.index = mcols(annotations)$txid, GENEIDs = GENEIDs.i, isoreParameters = isoreParameters,
322-
emParameters = emParameters, trackReads = trackReads,
321+
txid.index = mcols(annotations)$txid, GENEIDs = GENEIDs.i,
322+
emParameters = opt.em, trackReads = trackReads,
323323
verbose = verbose))},
324324
BPPARAM = bpParameters)
325325
end.ptm <- proc.time()

‎R/bambu_utilityFunctions.R‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -13,17 +13,17 @@ setBiocParallelParameters <- function(reads, ncore, verbose, demultiplexed){
1313
}
1414

1515

16-
#' setIsoreparameters
16+
#' setDiscoveryParameters
1717
#' @noRd
18-
setIsoreParameters <- function(isoreParameters){
18+
setDiscoveryParameters <- function(discoveryParameters){
1919
# ===# set default controlling parameters for isoform reconstruction #===#
20-
isoreParameters.default <- list(
21-
remove.subsetTx = TRUE,
20+
discoveryParameters.default <- list(
21+
remove.subsetTx = TRUE,
2222
min.readCount = 2,
2323
min.readFractionByGene = 0.05,
2424
min.sampleNumber = 1,
2525
min.exonDistance = 35,
26-
min.exonOverlap = 10,
26+
min.exonOverlap = 10,
2727
min.primarySecondaryDist = 5,
2828
min.primarySecondaryDistStartEnd1 = 5, # for creating new annotations
2929
min.primarySecondaryDistStartEnd2 = 5, # for read assignment
@@ -34,10 +34,10 @@ setIsoreParameters <- function(isoreParameters){
3434
returnModel = FALSE,
3535
baselineFDR = 0.1,
3636
min.readFractionByEqClass = 0,
37-
prefix = "Bambu")
38-
isoreParameters <-
39-
updateParameters(isoreParameters, isoreParameters.default)
40-
return(isoreParameters)
37+
prefix = "Bambu")
38+
discoveryParameters <-
39+
updateParameters(discoveryParameters, discoveryParameters.default)
40+
return(discoveryParameters)
4141
}
4242

4343

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