Commit id: 2155bb403810b2744c1ee1c364aa2fe6216a6671
bumped version
Commit id: f2df86b5e594d94aa0fd591152f9121554dfc47c
more work on permutations; now including unitTests
Commit id: 040af54e133c6fad141f3047a5b5a60772642b33
unit test for permutation matrix
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@100731 bc3139a8-67e5-0310-9ffc-ced21a209358
khansen authored on 16/03/2015 19:57:19
| ... | ... |
@@ -1,12 +1,12 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.3.6 |
|
| 2 |
+Version: 1.3.7 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data. |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 6 | 6 |
email = "kasperdanielhansen@gmail.com")) |
| 7 | 7 |
Depends: R (>= 2.15), methods, BiocGenerics, S4Vectors, IRanges (>= 2.1.10), |
| 8 | 8 |
GenomicRanges (>= 1.19.6), parallel, matrixStats, GenomeInfoDb |
| 9 |
-Imports: scales, stats, graphics, Biobase, locfit |
|
| 9 |
+Imports: scales, stats, graphics, Biobase, locfit, gtools |
|
| 10 | 10 |
Suggests: RUnit, bsseqData |
| 11 | 11 |
Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
| 12 | 12 |
utils.R read.bsmooth.R read.bismark.R BSmooth.R BSmooth.tstat.R dmrFinder.R |
| ... | ... |
@@ -27,6 +27,7 @@ importFrom(Biobase, "validMsg") |
| 27 | 27 |
importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo", "seqinfo<-", |
| 28 | 28 |
"seqnames", "seqnames<-", "seqlevels", "seqlevels<-") |
| 29 | 29 |
import(S4Vectors) |
| 30 |
+importFrom(gtools, "combinations") |
|
| 30 | 31 |
|
| 31 | 32 |
## |
| 32 | 33 |
## Exporting |
| ... | ... |
@@ -68,6 +68,7 @@ getFWER <- function(null, type = "blocks") {
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| 68 | 68 |
} |
| 69 | 69 |
|
| 70 | 70 |
makeIdxMatrix <- function(group1, group2, testIsSymmetric = TRUE, includeUnbalanced = TRUE) {
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+ ## gtools::combinations |
|
| 71 | 72 |
groupBoth <- c(group1, group2) |
| 72 | 73 |
idxMatrix1 <- NULL |
| 73 | 74 |
subsetByMatrix <- function(vec, mat) {
|
| ... | ... |
@@ -80,7 +81,10 @@ makeIdxMatrix <- function(group1, group2, testIsSymmetric = TRUE, includeUnbalan |
| 80 | 81 |
do.call(rbind, tmp) |
| 81 | 82 |
} |
| 82 | 83 |
if(length(group1) == 1 && length(group1) == 1) {
|
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- idxMatrix1 <- as.matrix(group1) |
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+ if(testIsSymmetric) |
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+ idxMatrix1 <- as.matrix(group1) |
|
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+ else |
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+ idxMatrix1 <- as.matrix(c(group1, group2)) |
|
| 84 | 88 |
} |
| 85 | 89 |
if(length(group1) == 2 && length(group2) == 2) {
|
| 86 | 90 |
if(testIsSymmetric) {
|
| ... | ... |
@@ -93,21 +97,28 @@ makeIdxMatrix <- function(group1, group2, testIsSymmetric = TRUE, includeUnbalan |
| 93 | 97 |
} |
| 94 | 98 |
} |
| 95 | 99 |
if(length(group1) == 3 && length(group1) == 3) {
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- newMatrix <- combineMat(subsetByMatrix(group1, combinations(3,2)), |
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- as.matrix(group2, ncol = 1)) |
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- idxMatrix1 <- rbind(group1, newMatrix) |
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- if(!testIsSymmetric) {
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- newMatrix <- combineMat(as.matrix(group1, ncol = 1), |
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- subsetByMatrix(group2, combinations(3,2))) |
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- idxMatrix1 <- rbind(idxMatrix1, group2, newMatrix) |
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+ if(testIsSymmetric) {
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+ idxMatrix1 <- rbind(group1, |
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+ combineMat(subsetByMatrix(group1, combinations(3,2)), |
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+ as.matrix(group2, ncol = 1))) |
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+ |
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+ } else {
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+ idxMatrix1 <- rbind(group1, group2, |
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+ combineMat(subsetByMatrix(group1, combinations(3,2)), |
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+ as.matrix(group2, ncol = 1)), |
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+ combineMat(as.matrix(group1, ncol = 1), |
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+ subsetByMatrix(group2, combinations(3,2)))) |
|
| 103 | 111 |
} |
| 104 | 112 |
} |
| 105 | 113 |
if(length(group1) == 4 && length(group1) == 4) {
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- newMatrix <- combineMat(subsetByMatrix(group1, combinations(4,2)), |
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- subsetByMatrix(group2, combinations(4,2))) |
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- idxMatrix1 <- rbind(group1, newMatrix) |
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- if(!testIsSymmetric) {
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- idxMatrix1 <- rbind(group2, idxMatrix1) |
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+ if(testIsSymmetric) {
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+ idxMatrix1 <- rbind(group1, |
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+ combineMat(subsetByMatrix(group1, combinations(3,2)), |
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+ subsetByMatrix(group2, combinations(4,2)))) |
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+ } else {
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+ idxMatrix1 <- rbind(group1, group2, |
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+ combineMat(subsetByMatrix(group1, combinations(4,2)), |
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+ subsetByMatrix(group2, combinations(4,2)))) |
|
| 111 | 122 |
} |
| 112 | 123 |
if(includeUnbalanced) {
|
| 113 | 124 |
newMatrix <- combineMat(subsetByMatrix(group1, combinations(4,3)), |
| ... | ... |
@@ -119,15 +130,29 @@ makeIdxMatrix <- function(group1, group2, testIsSymmetric = TRUE, includeUnbalan |
| 119 | 130 |
subsetByMatrix(group2, combinations(4,3))) |
| 120 | 131 |
idxMatrix1 <- rbind(idxMatrix1, newMatrix) |
| 121 | 132 |
} |
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- |
|
| 123 | 133 |
} |
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- if(length(group1) == 5 && length(group1) == 5 && testIsSymmetric) {
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- idxMatrix1 <- rbind(group1, |
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- combineMat(subsetByMatrix(group1, combinations(5, 3)), |
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- subsetByMatrix(group2, combinations(5, 2)))) |
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- if(includeUnbalanced) |
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+ if(length(group1) == 5 && length(group1) == 5) {
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+ if(testIsSymmetric) {
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+ idxMatrix1 <- rbind(group1, |
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+ combineMat(subsetByMatrix(group1, combinations(5, 3)), |
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+ subsetByMatrix(group2, combinations(5, 2)))) |
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+ } else {
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+ idxMatrix1 <- rbind(group1, group2, |
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+ combineMat(subsetByMatrix(group1, combinations(5, 3)), |
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+ subsetByMatrix(group2, combinations(5, 2))), |
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+ combineMat(subsetByMatrix(group1, combinations(5, 2)), |
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+ subsetByMatrix(group2, combinations(5, 3)))) |
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+ } |
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+ if(includeUnbalanced) {
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| 129 | 147 |
idxMatrix1 <- rbind(idxMatrix1, |
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- combineMat(subsetByMatrix(group1, combinations(5,4)), group2)) |
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+ combineMat(subsetByMatrix(group1, combinations(5,4)), |
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+ as.matrix(group2, ncol = 1))) |
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+ } |
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+ if(includeUnbalanced && !testIsSymmetric) {
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+ idxMatrix1 <- rbind(idxMatrix1, |
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+ combineMat(as.matrix(group1, ncol = 1), |
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+ subsetByMatrix(group2, combinations(5,4)))) |
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+ } |
|
| 131 | 156 |
} |
| 132 | 157 |
if(is.null(idxMatrix1)) |
| 133 | 158 |
stop("unable to handle this combination of 'group1', 'group2' and 'testIsSymmetric'")
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| 134 | 159 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,84 @@ |
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+test_makeIdxMatrix_perm1 <- function() {
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+ grp1 <- paste0("A", 1)
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+ grp2 <- paste0("B", 1)
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+ |
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+ res <- bsseq:::makeIdxMatrix(grp1, grp2, testIsSymmetric = FALSE)[[1]] |
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+ checkEquals(anyDuplicated(res), 0L) |
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+ checkEquals(res[1,], grp1) |
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+ checkEquals(res[2,], grp2) |
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+ checkEquals(nrow(res), choose(2,1)) # Fail |
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+ |
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+ res <- bsseq:::makeIdxMatrix(grp1, grp2, testIsSymmetric = TRUE)[[1]] |
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+ checkEquals(anyDuplicated(res), 0L) |
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+ checkEquals(res[1,], grp1) |
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+ checkEquals(nrow(res), choose(2,1) / 2) |
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+} |
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+ |
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+test_makeIdxMatrix_perm2 <- function() {
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+ grp1 <- paste0("A", 1:2)
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+ grp2 <- paste0("B", 1:2)
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+ |
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+ res <- bsseq:::makeIdxMatrix(grp1, grp2, testIsSymmetric = FALSE)[[1]] |
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+ checkEquals(anyDuplicated(res), 0) |
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+ checkEquals(res[1,], grp1) |
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+ checkEquals(res[2,], grp2) |
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+ checkEquals(nrow(res), choose(4,2)) |
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+ |
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+ res <- bsseq:::makeIdxMatrix(grp1, grp2, testIsSymmetric = TRUE)[[1]] |
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+ checkEquals(anyDuplicated(res), 0) |
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+ checkEquals(res[1,], grp1) |
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+ checkEquals(nrow(res), choose(4,2) / 2) |
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+} |
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+ |
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+test_makeIdxMatrix_perm3 <- function() {
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+ grp1 <- paste0("A", 1:3)
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+ grp2 <- paste0("B", 1:3)
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+ |
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+ res <- bsseq:::makeIdxMatrix(grp1, grp2, testIsSymmetric = FALSE)[[1]] |
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+ checkEquals(anyDuplicated(res), 0) |
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+ checkEquals(res[1,], grp1) |
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+ checkEquals(res[2,], grp2) |
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+ checkEquals(nrow(res), choose(6,3)) |
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+ |
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+ res <- bsseq:::makeIdxMatrix(grp1, grp2, testIsSymmetric = TRUE)[[1]] |
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+ checkEquals(anyDuplicated(res), 0) |
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+ checkEquals(res[1,], grp1) |
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+ checkEquals(nrow(res), choose(6,3) / 2) |
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+} |
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+ |
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+test_makeIdxMatrix_perm4 <- function() {
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+ grp1 <- paste0("A", 1:4)
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+ grp2 <- paste0("B", 1:4)
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+ |
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+ res <- bsseq:::makeIdxMatrix(grp1, grp2, |
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+ testIsSymmetric = FALSE, includeUnbalanced = TRUE)[[1]] |
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+ checkEquals(anyDuplicated(res), 0) |
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+ checkEquals(res[1,], grp1) |
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+ checkEquals(res[2,], grp2) |
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+ checkEquals(nrow(res), choose(8,4)) |
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+ |
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+ res <- bsseq:::makeIdxMatrix(grp1, grp2, |
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+ testIsSymmetric = TRUE, includeUnbalanced = TRUE)[[1]] |
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+ checkEquals(anyDuplicated(res), 0) |
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+ checkEquals(res[1,], grp1) |
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+ checkEquals(nrow(res), choose(8,4) / 2) # Fail |
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+} |
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+ |
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+test_makeIdxMatrix_perm5 <- function() {
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+ grp1 <- paste0("A", 1:5)
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+ grp2 <- paste0("B", 1:5)
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+ |
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+ res <- bsseq:::makeIdxMatrix(grp1, grp2, |
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+ testIsSymmetric = FALSE, includeUnbalanced = TRUE)[[1]] |
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+ checkEquals(anyDuplicated(res), 0) |
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+ checkEquals(res[1,], grp1) |
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+ checkEquals(res[2,], grp2) |
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+ checkEquals(nrow(res), choose(10,5)) |
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+ |
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+ res <- bsseq:::makeIdxMatrix(grp1, grp2, |
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+ testIsSymmetric = TRUE, includeUnbalanced = TRUE)[[1]] |
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+ checkEquals(anyDuplicated(res), 0) |
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+ checkEquals(res[1,], grp1) |
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+ checkEquals(nrow(res), choose(10,5) / 2) |
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+} |
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+ |