From e11e68e8e6486d09b1201258bad062fdeb2c3fad Mon Sep 17 00:00:00 2001 From: Astrid Deschenes Date: Fri, 29 Sep 2023 18:54:45 -0400 Subject: [PATCH 1/2] Update doc for addGeneBlockGDSRefAnnot() function --- R/process1KG.R | 22 ++++++++++++---------- man/addGeneBlockGDSRefAnnot.Rd | 22 ++++++++++++---------- 2 files changed, 24 insertions(+), 20 deletions(-) diff --git a/R/process1KG.R b/R/process1KG.R index 8d3a449b..a9595cfe 100644 --- a/R/process1KG.R +++ b/R/process1KG.R @@ -819,22 +819,24 @@ getRef1KGPop <- function(gdsReference, popName="superPop") { #' fileReferenceGDS <- file.path(dataDir, "tests", #' "ex1_good_small_1KG.gds") #' -#' ## Open the reference GDS file (demo version) -#' gds1KG <- snpgdsOpen(fileReferenceGDS) +#' \donttest{ +#' ## Open the reference GDS file (demo version) +#' gds1KG <- snpgdsOpen(fileReferenceGDS) #' -#' ## Append information associated to blocks -#' addGeneBlockGDSRefAnnot(gdsReference=gds1KG, +#' ## Append information associated to blocks +#' addGeneBlockGDSRefAnnot(gdsReference=gds1KG, #' gdsRefAnnotFile=fileAnnotGDS, #' ensDb=edb, #' suffixBlockName="EnsDb.Hsapiens.v86") #' -#' gdsAnnot1KG <- openfn.gds(fileAnnotGDS) -#' print(gdsAnnot1KG) -#' print(read.gdsn(index.gdsn(gdsAnnot1KG, "block.annot"))) +#' gdsAnnot1KG <- openfn.gds(fileAnnotGDS) +#' print(gdsAnnot1KG) +#' print(read.gdsn(index.gdsn(gdsAnnot1KG, "block.annot"))) #' -#' ## Close GDS files -#' closefn.gds(gds1KG) -#' closefn.gds(gdsAnnot1KG) +#' ## Close GDS files +#' closefn.gds(gds1KG) +#' closefn.gds(gdsAnnot1KG) +#' } #' #' ## Remove temporary file #' unlink(fileAnnotGDS, force=TRUE) diff --git a/man/addGeneBlockGDSRefAnnot.Rd b/man/addGeneBlockGDSRefAnnot.Rd index 0a414473..c8cd7902 100644 --- a/man/addGeneBlockGDSRefAnnot.Rd +++ b/man/addGeneBlockGDSRefAnnot.Rd @@ -65,22 +65,24 @@ if (requireNamespace("EnsDb.Hsapiens.v86", quietly=TRUE)) { fileReferenceGDS <- file.path(dataDir, "tests", "ex1_good_small_1KG.gds") - ## Open the reference GDS file (demo version) - gds1KG <- snpgdsOpen(fileReferenceGDS) + \donttest{ + ## Open the reference GDS file (demo version) + gds1KG <- snpgdsOpen(fileReferenceGDS) - ## Append information associated to blocks - addGeneBlockGDSRefAnnot(gdsReference=gds1KG, + ## Append information associated to blocks + addGeneBlockGDSRefAnnot(gdsReference=gds1KG, gdsRefAnnotFile=fileAnnotGDS, ensDb=edb, suffixBlockName="EnsDb.Hsapiens.v86") - gdsAnnot1KG <- openfn.gds(fileAnnotGDS) - print(gdsAnnot1KG) - print(read.gdsn(index.gdsn(gdsAnnot1KG, "block.annot"))) + gdsAnnot1KG <- openfn.gds(fileAnnotGDS) + print(gdsAnnot1KG) + print(read.gdsn(index.gdsn(gdsAnnot1KG, "block.annot"))) - ## Close GDS files - closefn.gds(gds1KG) - closefn.gds(gdsAnnot1KG) + ## Close GDS files + closefn.gds(gds1KG) + closefn.gds(gdsAnnot1KG) + } ## Remove temporary file unlink(fileAnnotGDS, force=TRUE) From 82f9a002016da069a8068eb62c287ab31188eed2 Mon Sep 17 00:00:00 2001 From: Astrid Deschenes Date: Fri, 29 Sep 2023 18:57:41 -0400 Subject: [PATCH 2/2] Update doc for generateGeneBloc() function --- R/process1KG_internal.R | 20 +++++++++++++------- man/generateGeneBlock.Rd | 18 ++++++++++++------ 2 files changed, 25 insertions(+), 13 deletions(-) diff --git a/R/process1KG_internal.R b/R/process1KG_internal.R index ac467ea6..597cf365 100644 --- a/R/process1KG_internal.R +++ b/R/process1KG_internal.R @@ -194,13 +194,19 @@ pruning1KGbyChr <- function(gdsReference, method="corr", listSamples=NULL, #' ## Reference GDS file #' fileReferenceGDS <- file.path(path1KG, "ex1_good_small_1KG.gds") #' -#' ## Open the reference GDS file (demo version) -#' gds1KG <- snpgdsOpen(fileReferenceGDS) -#' -#' ## The function returns a data frame containing gene block information -#' matGeneBlock <- RAIDS:::generateGeneBlock(gdsReference=gds1KG, ensDb=edb) -#' print(head(matGeneBlock[grep("ENSG00000157152", matGeneBlock$GName),])) -#' closefn.gds(gds1KG) +#' \donttest{ +#' ## Open the reference GDS file (demo version) +#' gds1KG <- snpgdsOpen(fileReferenceGDS) +#' +#' ## The function returns a data.frame containing +#' ## gene block information +#' matGeneBlock <- RAIDS:::generateGeneBlock(gdsReference=gds1KG, +#' ensDb=edb) +#' print(head(matGeneBlock[grep("ENSG00000157152", +#' matGeneBlock$GName),])) +#' +#' closefn.gds(gds1KG) +#' } #' } #' #' @author Pascal Belleau, Astrid Deschênes and Alex Krasnitz diff --git a/man/generateGeneBlock.Rd b/man/generateGeneBlock.Rd index 5dc672a0..0c800291 100644 --- a/man/generateGeneBlock.Rd +++ b/man/generateGeneBlock.Rd @@ -70,13 +70,19 @@ if (requireNamespace("EnsDb.Hsapiens.v86", quietly=TRUE)) { ## Reference GDS file fileReferenceGDS <- file.path(path1KG, "ex1_good_small_1KG.gds") - ## Open the reference GDS file (demo version) - gds1KG <- snpgdsOpen(fileReferenceGDS) + \donttest{ + ## Open the reference GDS file (demo version) + gds1KG <- snpgdsOpen(fileReferenceGDS) - ## The function returns a data frame containing gene block information - matGeneBlock <- RAIDS:::generateGeneBlock(gdsReference=gds1KG, ensDb=edb) - print(head(matGeneBlock[grep("ENSG00000157152", matGeneBlock$GName),])) - closefn.gds(gds1KG) + ## The function returns a data.frame containing + ## gene block information + matGeneBlock <- RAIDS:::generateGeneBlock(gdsReference=gds1KG, + ensDb=edb) + print(head(matGeneBlock[grep("ENSG00000157152", + matGeneBlock$GName),])) + + closefn.gds(gds1KG) + } } }