Package: RAIDS
Authors: Pascal Belleau [cre, aut] (https://orcid.org/0000-0002-0802-1071), Astrid Deschênes
[aut] (https://orcid.org/0000-0001-7846-6749), David A. Tuveson
[aut] (https://orcid.org/0000-0002-8017-2712), Alexander
-Krasnitz [aut]
Version: 1.3.2
Compiled date: 2024-10-16
License: Apache License (>= 2)
This vignette explains, in further details, the format of the population reference files that are required to run the ancestry @@ -393,7 +393,7 @@
Package: RAIDS
Authors: Pascal Belleau [cre, aut] (https://orcid.org/0000-0002-0802-1071), Astrid Deschênes
[aut] (https://orcid.org/0000-0001-7846-6749), David A. Tuveson
[aut] (https://orcid.org/0000-0002-8017-2712), Alexander
-Krasnitz [aut]
Version: 1.3.2
Compiled date: 2024-10-16
License: Apache License (>= 2)
First, a specific directory structure should be created. The
-structure must
-correspond to this:
#############################################################################
## Working directory structure
@@ -198,8 +197,8 @@ 1.1 Create a directory structurerefGDS
profileGDS
This following running example creates a temporary working directory -structure when the example will be run.
+This following code creates a temporary working directory structure +where the example will be run.
#############################################################################
@@ -337,11 +336,42 @@ 2.3 Perform the ancestry inference
According to the type of input data (RNA or DNA), a specific function
-is available.
-The inferAncestry() function is used for DNA profiles while
-the inferAncestryGeneAware() function is RNA specific.
+is available. The inferAncestry() function is used for DNA
+profiles while the inferAncestryGeneAware() function is RNA
+specific.
In this example, the profile is from DNA source and requires the use
of the inferAncestry() function.
+The inferAncestry() function requires a specific profile
+input format. The format is set by the genoSource
+parameter.
+One of those formats is in a VCF format
+(genoSource=c(“VCF”)). This format follows the VCF standard
+with at least those genotype fields: GT, AD and
+DP. The SNVs must be germline variants and should include the
+genotype of the wild-type homozygous at the selected positions in the
+reference. The VCF file must be gzipped.
+A generic SNP file can replace the VCF file
+(genoSource=c(“generic”)). The format is coma separated and the
+mandatory columns are:
+
+-
+Chromosome: The name of the chromosome
+-
+Position: The position on the chromosome
+-
+Ref: The reference nucleotide
+-
+Alt: The aternative nucleotide
+-
+Count: The total count
+-
+File1R: The count for the reference nucleotide
+-
+File1A: The count for the alternative nucleotide
+
+Beware that the starting position in the population reference
+GDS file is zero (like BED files). The generic SNP file should
+also start at position zero.
###########################################################################
@@ -358,7 +388,7 @@ 2.3 Perform the ancestry inference chrInfo <- GenomeInfoDb::seqlengths(genome)[1:25]
#######################################################################
- ## The SNP VCF file of the DNA profile donor
+ ## The demo SNP VCF file of the DNA profile donor
#######################################################################
fileDonorVCF <- file.path(dataDir, "example", "snpPileup", "ex1.vcf.gz")
diff --git a/articles/Wrappers.html b/articles/Wrappers.html
index d744c853..7b549125 100644
--- a/articles/Wrappers.html
+++ b/articles/Wrappers.html
@@ -95,7 +95,7 @@ Pascal Belleau,
Package: RAIDS
Authors: Pascal Belleau [cre, aut] (https://orcid.org/0000-0002-0802-1071), Astrid Deschênes
[aut] (https://orcid.org/0000-0001-7846-6749), David A. Tuveson
[aut] (https://orcid.org/0000-0002-8017-2712), Alexander
-Krasnitz [aut]
Version: 1.3.2
Compiled date: 2024-10-16
License: Apache License (>= 2)
+Krasnitz [aut]
Version: 1.3.2
Compiled date: 2024-10-21
License: Apache License (>= 2)
This vignette explains, in further details, the used of the wrapper
functions that were developed for a previous release of RAIDS.
diff --git a/pkgdown.yml b/pkgdown.yml
index eaf47179..da542f31 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,4 +5,4 @@ articles:
Create_Reference_GDS_File: Create_Reference_GDS_File.html
RAIDS: RAIDS.html
Wrappers: Wrappers.html
-last_built: 2024-10-16T21:30Z
+last_built: 2024-10-21T23:19Z
diff --git a/reference/add1KG2SampleGDS.html b/reference/add1KG2SampleGDS.html
index 3d802f7e..8cb6d737 100644
--- a/reference/add1KG2SampleGDS.html
+++ b/reference/add1KG2SampleGDS.html
@@ -154,7 +154,7 @@ Examples
## The 'pruned.study' entry should be present
content <- openfn.gds(fileProfile)
content
-#> File: /tmp/RtmptZiY8e/ex2.gds (10.4K)
+#> File: /tmp/RtmpZ7wD2p/ex2.gds (10.4K)
#> + [ ]
#> |--+ Ref.count { SparseInt16 11000x1, 568B }
#> |--+ Alt.count { SparseInt16 11000x1, 74B }
diff --git a/reference/addBlockFromDetFile.html b/reference/addBlockFromDetFile.html
index 243dbc95..7a113e56 100644
--- a/reference/addBlockFromDetFile.html
+++ b/reference/addBlockFromDetFile.html
@@ -179,7 +179,7 @@ Examples
gdsAnnot1KG <- openfn.gds(fileAnnotGDS)
print(gdsAnnot1KG)
-#> File: /tmp/RtmptZiY8e/ex1_good_small_1KG_Ann_GDS.gds (349.4K)
+#> File: /tmp/RtmpZ7wD2p/ex1_good_small_1KG_Ann_GDS.gds (349.4K)
#> + [ ]
#> |--+ phase { Bit2 11000x156 LZ4_ra(21.5%), 90.2K }
#> |--+ block.annot [ data.frame ] *
diff --git a/reference/addGDS1KGLDBlock.html b/reference/addGDS1KGLDBlock.html
index 210312e8..d4ab7587 100644
--- a/reference/addGDS1KGLDBlock.html
+++ b/reference/addGDS1KGLDBlock.html
@@ -143,7 +143,7 @@ Examples
gdsAnnot1KG <- openfn.gds(fileAnnotGDS)
print(gdsAnnot1KG)
-#> File: /tmp/RtmptZiY8e/ex1_good_small_1KG_Ann_GDS.gds (349.4K)
+#> File: /tmp/RtmpZ7wD2p/ex1_good_small_1KG_Ann_GDS.gds (349.4K)
#> + [ ]
#> |--+ phase { Bit2 11000x156 LZ4_ra(21.5%), 90.2K }
#> |--+ block.annot [ data.frame ] *
diff --git a/reference/addGeneBlockGDSRefAnnot.html b/reference/addGeneBlockGDSRefAnnot.html
index 5b25e5ae..fcdbda41 100644
--- a/reference/addGeneBlockGDSRefAnnot.html
+++ b/reference/addGeneBlockGDSRefAnnot.html
@@ -168,7 +168,7 @@ Examples
unlink(fileAnnotGDS, force=TRUE)
}
-#> File: /tmp/RtmptZiY8e/ex1_good_small_1KG_Ann_GDS.gds (392.5K)
+#> File: /tmp/RtmpZ7wD2p/ex1_good_small_1KG_Ann_GDS.gds (392.5K)
#> + [ ]
#> |--+ phase { Bit2 11000x156 LZ4_ra(21.5%), 90.2K }
#> |--+ block.annot [ data.frame ] *
diff --git a/reference/addGeneBlockRefAnnot.html b/reference/addGeneBlockRefAnnot.html
index 537eb5b2..179f97f8 100644
--- a/reference/addGeneBlockRefAnnot.html
+++ b/reference/addGeneBlockRefAnnot.html
@@ -162,7 +162,7 @@ Examples
unlink(fileAnnotGDS, force=TRUE)
}
-#> File: /tmp/RtmptZiY8e/ex1_good_small_1KG_Ann_GDS.gds (392.5K)
+#> File: /tmp/RtmpZ7wD2p/ex1_good_small_1KG_Ann_GDS.gds (392.5K)
#> + [ ]
#> |--+ phase { Bit2 11000x156 LZ4_ra(21.5%), 90.2K }
#> |--+ block.annot [ data.frame ] *
diff --git a/reference/addStudy1Kg.html b/reference/addStudy1Kg.html
index 9611f28b..77014493 100644
--- a/reference/addStudy1Kg.html
+++ b/reference/addStudy1Kg.html
@@ -156,7 +156,7 @@ Examples
## The Profile GDS file will contain 'study.list' and 'study.annot' entries
addStudy1Kg(gdsReference=gds1KG, fileProfileGDS=fileNameProfile,
verbose=TRUE)
-#> study.annot DONE 2024-10-16 21:31:26.762997
+#> study.annot DONE 2024-10-21 23:20:36.957532
#> [1] 0
closefn.gds(gds1KG)
diff --git a/reference/createStudy2GDS1KG.html b/reference/createStudy2GDS1KG.html
index 068396e0..4c1be5df 100644
--- a/reference/createStudy2GDS1KG.html
+++ b/reference/createStudy2GDS1KG.html
@@ -223,7 +223,7 @@ Examples
## The Profile GDS file 'ex1.gds' has been created in the
## specified directory
list.files(tempdir())
-#> [1] "downlit" "ex1.gds" "filebb5394c14ac"
+#> [1] "downlit" "ex1.gds" "filebc74c76775f"
## Remove Profile GDS file (created for demo purpose)
unlink(file.path(tempdir(), "ex1.gds"), force=TRUE)
diff --git a/reference/generateGDS1KGgenotypeFromSNPPileup.html b/reference/generateGDS1KGgenotypeFromSNPPileup.html
index 81a0b467..6bf1a1d7 100644
--- a/reference/generateGDS1KGgenotypeFromSNPPileup.html
+++ b/reference/generateGDS1KGgenotypeFromSNPPileup.html
@@ -239,7 +239,7 @@ Examples
## The Profile GDS file 'ex1.gds' has been created in the
## specified directory
list.files(dataDir)
-#> [1] "downlit" "ex1.gds" "ex1.txt.gz" "filebb5394c14ac"
+#> [1] "downlit" "ex1.gds" "ex1.txt.gz" "filebc74c76775f"
## Unlink Profile GDS file (created for demo purpose)
unlink(file.path(dataDir, "ex1.gds"))
diff --git a/reference/generateGDSSNPinfo.html b/reference/generateGDSSNPinfo.html
index 660777f9..78b37bea 100644
--- a/reference/generateGDSSNPinfo.html
+++ b/reference/generateGDSSNPinfo.html
@@ -116,12 +116,12 @@ Examples
## Add SNV information to Reference GDS
RAIDS:::generateGDSSNPinfo(gdsReference=filenewGDS,
fileFreq=fileFilerterSNVs, verbose=TRUE)
-#> Read mapSNVSel DONE 2024-10-16 21:31:51.071898
-#> SNP part snp.id DONE 2024-10-16 21:31:51.07243
-#> SNP part snp.chromosome DONE 2024-10-16 21:31:51.072845
-#> SNP part snp.position DONE 2024-10-16 21:31:51.07323
-#> SNP part 1 DONE 2024-10-16 21:31:51.073617
-#> SNP part AF DONE 2024-10-16 21:31:51.073994
+#> Read mapSNVSel DONE 2024-10-21 23:21:00.83511
+#> SNP part snp.id DONE 2024-10-21 23:21:00.835595
+#> SNP part snp.chromosome DONE 2024-10-21 23:21:00.83602
+#> SNP part snp.position DONE 2024-10-21 23:21:00.836411
+#> SNP part 1 DONE 2024-10-21 23:21:00.836827
+#> SNP part AF DONE 2024-10-21 23:21:00.837214
#> [1] 0
## Close GDS file (important)
diff --git a/reference/pruningSample.html b/reference/pruningSample.html
index 309fa932..607a8234 100644
--- a/reference/pruningSample.html
+++ b/reference/pruningSample.html
@@ -260,7 +260,7 @@ Examples
## The 'pruned.study' entry should be present
content <- openfn.gds(profileFile)
content
-#> File: /tmp/RtmptZiY8e/ex1.gds (4.3K)
+#> File: /tmp/RtmpZ7wD2p/ex1.gds (4.3K)
#> + [ ]
#> |--+ Ref.count { SparseInt16 11000x1, 568B }
#> |--+ Alt.count { SparseInt16 11000x1, 74B }