Last updated: 26 July, 2024
Source:vignettes/rCNV.Rmd
@@ -111,7 +111,12 @@
starting with raw (unfiltered) VCF as in the number 1 of the workflow
chart. However, if one believes that they have filtered VCFs for the
parameters we highlight (see Fig.1 and sub-sections 1.2 and 1.3), they
-can start from the number 2 in the workflow shown above.
+can start from the number 2 in the workflow shown above.
NOTE: In the latest iteration of the rCNV package, the
+functions sig.hets() and dupGet() use use a
+sample based inbreeding coefficient (Fis) to improve the
+accuracy of the deviant detection. This Fis is calculated using
+the h.zygosity() function; see below for more
+information.
# Start by installing the package if you haven't already done so.
# To install the CRAN version
@@ -703,7 +708,7 @@ 2.2 Deviants detection
# Run this code for a demonstration of the detection
-dvs<-dupGet(alleleINF,test = c("z.05","chi.05"))
+dvs<-dupGet(alleleINF,test = c("z.05","chi.05"),Fis=0.11)
# z score and chi-square values given p=0.05 is used here because the data is RADseq generated and probe-biase is neglegible
head(dvs)
@@ -730,7 +735,11 @@ 2.2 Deviants detectionhttps://doi.org/10.1101/2022.10.14.512217 for more
details on probe bias.
-deviants<-dupGet(alleleINF,test = c("z.all","chi.all"),plot=TRUE,verbose = TRUE)
+# in the new version of the package dupGet function requires Fis value for a more accurate detection of the deviants
+# this is obtained by using the h.zygosity() function as below
+hz<-h.zygosity(parrot,verbose = FALSE) #parrot is the filtered vcf file
+Fis<-mean(hz$Fis,na.rm = TRUE)
+deviants<-dupGet(alleleINF,Fis=Fis,test = c("z.all","chi.all"),plot=TRUE,verbose = TRUE)
head(deviants)
#> CHROM POS ID NHet propHet medRatio NHomRef NHomAlt propHomAlt
#> 7452 un 705339 67808 9 0.08653846 0.5000000 95 0 0.00000000
diff --git a/docs/exVcf.vcf.gz b/docs/exVcf.vcf.gz
new file mode 100644
index 0000000..75f5f56
Binary files /dev/null and b/docs/exVcf.vcf.gz differ
diff --git a/docs/news/index.html b/docs/news/index.html
index af926b4..a3bc60c 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -49,7 +49,10 @@
rCNV 1.3.0 (third update)
-- vstPermutation function added
+- parallelization enabled
+- dupValidate function revised
+- per site Fis added to deviant detection
+- vstPermutation function added
- maf modified to remove multi-allelic sites
- FIT correction added
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 4c6ba03..ecafb35 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
pkgdown_sha: ~
articles:
rCNV: rCNV.html
-last_built: 2024-04-29T12:37Z
+last_built: 2024-07-26T08:56Z
diff --git a/docs/reference/ad.correct.html b/docs/reference/ad.correct.html
index 892b3b1..06084d8 100644
--- a/docs/reference/ad.correct.html
+++ b/docs/reference/ad.correct.html
@@ -69,7 +69,13 @@
Usage
- ad.correct(het.table, gt.table = NULL, odd.correct = TRUE, verbose = TRUE)
+ ad.correct(
+ het.table,
+ gt.table = NULL,
+ odd.correct = TRUE,
+ verbose = TRUE,
+ parallel = FALSE
+)
@@ -91,6 +97,10 @@ Arguments
Value
diff --git a/docs/reference/allele.freq.html b/docs/reference/allele.freq.html
index cae1f77..cf4a460 100644
--- a/docs/reference/allele.freq.html
+++ b/docs/reference/allele.freq.html
@@ -96,10 +96,10 @@ Examplesvcf <- readVCF(vcf.file.path=vcf.file.path)
het.table<-hetTgen(vcf,"GT")
#> generating table
-#>
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+#>
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ad.table<-hetTgen(vcf,"AD")
#> generating table
-#>
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+#>
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# for individual based AF
frQ<-allele.freq(het.table,f.typ="ind")
diff --git a/docs/reference/allele.info.html b/docs/reference/allele.info.html
index 2eb63e4..bae7ca4 100644
--- a/docs/reference/allele.info.html
+++ b/docs/reference/allele.info.html
@@ -63,6 +63,7 @@ Usage
allele.info(
X,
x.norm = NULL,
+ Fis,
method = c("MedR", "QN", "pca", "TMM", "TMMex"),
logratioTrim = 0.3,
sumTrim = 0.05,
@@ -70,6 +71,7 @@ Usage
Acutoff = -1e+10,
plot.allele.cov = TRUE,
verbose = TRUE,
+ parallel = FALSE,
...
)
@@ -86,6 +88,10 @@ Argumentsh.zygosity()
function
+
+
method
character. method to be used for normalization
(see cpm.normal details). Default TMM
ArgumentsExamples#> calculating chi-square significance
#>
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#> assessing excess of heterozygotes
+#> Error in allele.info(ADtable, x.norm = ADnorm): argument "Fis" is missing, with no default
-#>
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diff --git a/docs/reference/cnv.html b/docs/reference/cnv.html
index 92bfd8f..c8961a8 100644
--- a/docs/reference/cnv.html
+++ b/docs/reference/cnv.html
@@ -87,11 +87,7 @@ ArgumentsDetails
+WGS is a test parameter to include or exclude coefficient of variance
+(cv) in kmeans. For data sets with more homogeneous depth distribution,
+excluding cv improves CNV detection. If you're not certain about this, use
+TRUE which is the default.
diff --git a/docs/reference/dup.validate.html b/docs/reference/dup.validate.html
index a24b574..e92d26d 100644
--- a/docs/reference/dup.validate.html
+++ b/docs/reference/dup.validate.html
@@ -1,6 +1,6 @@
-Validate detected duplicates — dup.validate • rCNV Validate detected deviants/cnvs — dup.validate • rCNV
# Start by installing the package if you haven't already done so.
# To install the CRAN version
@@ -703,7 +708,7 @@ 2.2 Deviants detection
# Run this code for a demonstration of the detection
-dvs<-dupGet(alleleINF,test = c("z.05","chi.05"))
+dvs<-dupGet(alleleINF,test = c("z.05","chi.05"),Fis=0.11)
# z score and chi-square values given p=0.05 is used here because the data is RADseq generated and probe-biase is neglegible
head(dvs)
-deviants<-dupGet(alleleINF,test = c("z.all","chi.all"),plot=TRUE,verbose = TRUE)
+# in the new version of the package dupGet function requires Fis value for a more accurate detection of the deviants
+# this is obtained by using the h.zygosity() function as below
+hz<-h.zygosity(parrot,verbose = FALSE) #parrot is the filtered vcf file
+Fis<-mean(hz$Fis,na.rm = TRUE)
+deviants<-dupGet(alleleINF,Fis=Fis,test = c("z.all","chi.all"),plot=TRUE,verbose = TRUE)
head(deviants)#> CHROM POS ID NHet propHet medRatio NHomRef NHomAlt propHomAlt
#> 7452 un 705339 67808 9 0.08653846 0.5000000 95 0 0.00000000
diff --git a/docs/exVcf.vcf.gz b/docs/exVcf.vcf.gz
new file mode 100644
index 0000000..75f5f56
Binary files /dev/null and b/docs/exVcf.vcf.gz differ
diff --git a/docs/news/index.html b/docs/news/index.html
index af926b4..a3bc60c 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -49,7 +49,10 @@
rCNV 1.3.0 (third update)
-- vstPermutation function added
+- parallelization enabled
+- dupValidate function revised
+- per site Fis added to deviant detection
+- vstPermutation function added
- maf modified to remove multi-allelic sites
- FIT correction added
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 4c6ba03..ecafb35 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
pkgdown_sha: ~
articles:
rCNV: rCNV.html
-last_built: 2024-04-29T12:37Z
+last_built: 2024-07-26T08:56Z
diff --git a/docs/reference/ad.correct.html b/docs/reference/ad.correct.html
index 892b3b1..06084d8 100644
--- a/docs/reference/ad.correct.html
+++ b/docs/reference/ad.correct.html
@@ -69,7 +69,13 @@
Usage
- ad.correct(het.table, gt.table = NULL, odd.correct = TRUE, verbose = TRUE)
+ ad.correct(
+ het.table,
+ gt.table = NULL,
+ odd.correct = TRUE,
+ verbose = TRUE,
+ parallel = FALSE
+)
@@ -91,6 +97,10 @@ Arguments
Value
diff --git a/docs/reference/allele.freq.html b/docs/reference/allele.freq.html
index cae1f77..cf4a460 100644
--- a/docs/reference/allele.freq.html
+++ b/docs/reference/allele.freq.html
@@ -96,10 +96,10 @@ Examplesvcf <- readVCF(vcf.file.path=vcf.file.path)
het.table<-hetTgen(vcf,"GT")
#> generating table
-#>
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+#>
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ad.table<-hetTgen(vcf,"AD")
#> generating table
-#>
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+#>
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# for individual based AF
frQ<-allele.freq(het.table,f.typ="ind")
diff --git a/docs/reference/allele.info.html b/docs/reference/allele.info.html
index 2eb63e4..bae7ca4 100644
--- a/docs/reference/allele.info.html
+++ b/docs/reference/allele.info.html
@@ -63,6 +63,7 @@ Usage
allele.info(
X,
x.norm = NULL,
+ Fis,
method = c("MedR", "QN", "pca", "TMM", "TMMex"),
logratioTrim = 0.3,
sumTrim = 0.05,
@@ -70,6 +71,7 @@ Usage
Acutoff = -1e+10,
plot.allele.cov = TRUE,
verbose = TRUE,
+ parallel = FALSE,
...
)
@@ -86,6 +88,10 @@ Argumentsh.zygosity()
function
+
+
character. method to be used for normalization
(see cpm.normal details). Default TMM
ArgumentsExamples#> calculating chi-square significance
#>
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#> assessing excess of heterozygotes
+#> Error in allele.info(ADtable, x.norm = ADnorm): argument "Fis" is missing, with no default
-#>
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diff --git a/docs/reference/cnv.html b/docs/reference/cnv.html
index 92bfd8f..c8961a8 100644
--- a/docs/reference/cnv.html
+++ b/docs/reference/cnv.html
@@ -87,11 +87,7 @@ ArgumentsDetails
+WGS is a test parameter to include or exclude coefficient of variance
+(cv) in kmeans. For data sets with more homogeneous depth distribution,
+excluding cv improves CNV detection. If you're not certain about this, use
+TRUE which is the default.
diff --git a/docs/reference/dup.validate.html b/docs/reference/dup.validate.html
index a24b574..e92d26d 100644
--- a/docs/reference/dup.validate.html
+++ b/docs/reference/dup.validate.html
@@ -1,6 +1,6 @@
-Validate detected duplicates — dup.validate • rCNV Validate detected deviants/cnvs — dup.validate • rCNV
WGS is a test parameter to include or exclude coefficient of variance
+(cv) in kmeans. For data sets with more homogeneous depth distribution,
+excluding cv improves CNV detection. If you're not certain about this, use
+TRUE which is the default.
diff --git a/docs/reference/dup.validate.html b/docs/reference/dup.validate.html
index a24b574..e92d26d 100644
--- a/docs/reference/dup.validate.html
+++ b/docs/reference/dup.validate.html
@@ -1,6 +1,6 @@
-Validate detected duplicates — dup.validate • rCNV Validate detected deviants/cnvs — dup.validate • rCNV