| ... | ... |
@@ -197,6 +197,25 @@ normalDB.min.coverage, normalDB.max.missing) {
|
| 197 | 197 |
intervalsUsed |
| 198 | 198 |
} |
| 199 | 199 |
|
| 200 |
+.filterIntervalsAllosome <- function(intervalsUsed, tumor, sex) {
|
|
| 201 |
+ if (is.null(sex)) return(intervalsUsed) |
|
| 202 |
+ sex.chr <- .getSexChr(seqlevels(tumor)) |
|
| 203 |
+ remove.chrs <- c() |
|
| 204 |
+ if (sex == "M" || sex == "?") {
|
|
| 205 |
+ remove.chrs <- sex.chr |
|
| 206 |
+ } else if (sex == "F") {
|
|
| 207 |
+ remove.chrs <- sex.chr[2] |
|
| 208 |
+ } |
|
| 209 |
+ nBefore <- sum(intervalsUsed) |
|
| 210 |
+ intervalsUsed <- intervalsUsed & !seqnames(tumor) %in% remove.chrs |
|
| 211 |
+ nAfter <- sum(intervalsUsed) |
|
| 212 |
+ if (nAfter < nBefore) {
|
|
| 213 |
+ flog.info("Removing %i non-diploid allosome intervals.", nBefore - nAfter)
|
|
| 214 |
+ } |
|
| 215 |
+ intervalsUsed |
|
| 216 |
+} |
|
| 217 |
+ |
|
| 218 |
+ |
|
| 200 | 219 |
.filterIntervalsTotalNormalCoverage <- function(intervalsUsed, normal, |
| 201 | 220 |
min.targeted.base, min.coverage) {
|
| 202 | 221 |
if (is.null(min.targeted.base) || is.null(min.coverage)) {
|
| ... | ... |
@@ -416,11 +416,10 @@ runAbsoluteCN <- function(normal.coverage.file = NULL, |
| 416 | 416 |
} |
| 417 | 417 |
|
| 418 | 418 |
sex <- .getSex(match.arg(sex), normal, tumor) |
| 419 |
- tumor <- .fixAllosomeCoverage(sex, tumor) |
|
| 420 |
- |
|
| 421 | 419 |
if (!is.null(interval.file)) {
|
| 422 | 420 |
tumor <- .addGCData(tumor, interval.file) |
| 423 | 421 |
} |
| 422 |
+ |
|
| 424 | 423 |
if (is.null(centromeres) && !missing(genome)) {
|
| 425 | 424 |
centromeres <- .getCentromerePositions(centromeres, genome, |
| 426 | 425 |
if (is.null(tumor)) NULL else .getSeqlevelsStyle(tumor)) |
| ... | ... |
@@ -442,6 +441,16 @@ runAbsoluteCN <- function(normal.coverage.file = NULL, |
| 442 | 441 |
# chr.hash is an internal data structure, so we need to do this separately. |
| 443 | 442 |
intervalsUsed <- .filterIntervalsChrHash(intervalsUsed, tumor, chr.hash) |
| 444 | 443 |
intervalsUsed <- .filterIntervalsCentromeres(intervalsUsed, tumor, centromeres) |
| 444 |
+ intervalsUsedAllosome <- intervalsUsed |
|
| 445 |
+ intervalsUsed <- .filterIntervalsAllosome(intervalsUsed, tumor, sex) |
|
| 446 |
+ |
|
| 447 |
+ if (!is.null(normalDB$sd$weights)) {
|
|
| 448 |
+ tumor$weights <- subsetByOverlaps(normalDB$sd$weights, tumor)$weights |
|
| 449 |
+ } |
|
| 450 |
+ tumorAllosome <- tumor |
|
| 451 |
+ tumorAllosome$log.ratio <- log.ratio |
|
| 452 |
+ tumorAllosome <- tumorAllosome[!intervalsUsed & intervalsUsedAllosome, ] |
|
| 453 |
+ |
|
| 445 | 454 |
intervalsUsed <- which(intervalsUsed) |
| 446 | 455 |
if (length(tumor) != length(normal) || |
| 447 | 456 |
length(tumor) != length(log.ratio)) {
|
| ... | ... |
@@ -468,9 +477,6 @@ runAbsoluteCN <- function(normal.coverage.file = NULL, |
| 468 | 477 |
flog.info("Mean off-target bin size: %.0f",
|
| 469 | 478 |
mean(width(tumor[!tumor$on.target]), na.rm = TRUE)) |
| 470 | 479 |
} |
| 471 |
- if (!is.null(normalDB$sd$weights)) {
|
|
| 472 |
- tumor$weights <- subsetByOverlaps(normalDB$sd$weights, tumor)$weights |
|
| 473 |
- } |
|
| 474 | 480 |
# not needed anymore |
| 475 | 481 |
normalDB <- NULL |
| 476 | 482 |
|
| ... | ... |
@@ -1145,7 +1151,7 @@ runAbsoluteCN <- function(normal.coverage.file = NULL, |
| 1145 | 1151 |
list( |
| 1146 | 1152 |
candidates = candidate.solutions, |
| 1147 | 1153 |
results = results, |
| 1148 |
- input = list(tumor = tumor.coverage.file, normal = normal.coverage.file, |
|
| 1154 |
+ input = list(tumor = tumor.coverage.file, normal = normal.coverage.file, allosome = tumorAllosome, |
|
| 1149 | 1155 |
log.ratio = GRanges(normal[, 1], on.target = normal$on.target, log.ratio = log.ratio), |
| 1150 | 1156 |
log.ratio.sdev = sd.seg, mapd = mapd, vcf = vcf, sampleid = sampleid, |
| 1151 | 1157 |
test.num.copy = test.num.copy, |
