diff --git a/404.html b/404.html index 85c3f72..562cf53 100644 --- a/404.html +++ b/404.html @@ -24,7 +24,7 @@ rPHG2 - 0.5 + 0.6 + + + + + +
+
+
+ +

Return number of haplotypes

+ Source: R/class_all_generics.R, R/class_phg_dataset.R +
numberOfHaplotypes.Rd
+
+ +
+

Returns the number of haplotypes either for the whole dataset or by each +individual reference range.

+
+ +
+

Usage

+ 
numberOfHaplotypes(object, ...)
+
+# S4 method for class 'PHGDataSet'
+numberOfHaplotypes(object, byRefRange = FALSE)
+
+ +
+

Arguments

+ + +
object
+

A PHGDataSet object

+ + +
...
+

Additional arguments, for use in specific methods

+ + +
byRefRange
+

If TRUE, a tibble object will created where each row is a +count of unique haplotype IDs for every reference range. If FALSE, a +global count of all haplotype IDs will be returned from the dataset.

+ +
+ +
+ + +
+ + + + + + + diff --git a/reference/numberOfRefRanges,PHGDataSet-method.html b/reference/numberOfRefRanges,PHGDataSet-method.html new file mode 100644 index 0000000..50c704f --- /dev/null +++ b/reference/numberOfRefRanges,PHGDataSet-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/numberOfRefRanges.html b/reference/numberOfRefRanges.html index fab7c83..3e2e6df 100644 --- a/reference/numberOfRefRanges.html +++ b/reference/numberOfRefRanges.html @@ -7,7 +7,7 @@ rPHG2 - 0.5 + 0.6 + + + + + +
+
+
+ +

Return number of samples

+ Source: R/class_all_generics.R, R/class_haplotype_graph.R, R/class_phg_dataset.R +
numberOfSamples.Rd
+
+ +
+

Returns the number of samples for a given object

+
+ +
+

Usage

+ 
numberOfSamples(object, ...)
+
+# S4 method for class 'HaplotypeGraph'
+numberOfSamples(object)
+
+# S4 method for class 'PHGDataSet'
+numberOfSamples(object)
+
+ +
+

Arguments

+ + +
object
+

an rPHG2 local or server connection object

+ + +
...
+

Additional arguments, for use in specific methods

+ + +
numberOfSamples
+

A character vector of sample IDs

+ +
+ +
+ + +
+ + + + + + + diff --git a/reference/phgType.html b/reference/phgType.html index 9053705..964712e 100644 --- a/reference/phgType.html +++ b/reference/phgType.html @@ -1,5 +1,7 @@ -Return type of PHG connection — phgType • rPHG2 +Return type of PHG connection — phgType • rPHG2 Skip to contents @@ -7,7 +9,7 @@ rPHG2 - 0.5 + 0.6 + + + + + +
+
+
+ +

Plot haplotype counts

+ Source: R/class_all_generics.R, R/class_phg_dataset.R +
plotHaploCounts.Rd
+
+ +
+

Plots the counts of unique haplotype IDs found in each reference range.

+
+ +
+

Usage

+ 
plotHaploCounts(object, ...)
+
+# S4 method for class 'PHGDataSet'
+plotHaploCounts(object, gr = NULL)
+
+ +
+

Arguments

+ + +
object
+

a PHGDataSet object

+ + +
...
+

Additional arguments, for use in specific methods

+ + +
gr
+

A GenomicRanges object for subsetting based on chromosome ID and +start/stop positions (bp). If NULL, all haplotype counts will be +plotted similar to a Manhattan plot. Defaults to NULL.

+ +
+ +
+ + +
+ + + + + + + diff --git a/reference/plotHaploDist,PHGDataSet-method.html b/reference/plotHaploDist,PHGDataSet-method.html new file mode 100644 index 0000000..eb79e62 --- /dev/null +++ b/reference/plotHaploDist,PHGDataSet-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/plotHaploDist.html b/reference/plotHaploDist.html new file mode 100644 index 0000000..fd4eceb --- /dev/null +++ b/reference/plotHaploDist.html @@ -0,0 +1,93 @@ + +Plot haplotype distribution — plotHaploDist • rPHG2 + Skip to contents + + +
+
+
+ +

Plot haplotype distribution

+ Source: R/class_all_generics.R, R/class_phg_dataset.R +
plotHaploDist.Rd
+
+ +
+

Plots a general distribution of the number of unique haplotypes in a +PHGDataSet object.

+
+ +
+

Usage

+ 
plotHaploDist(object, ...)
+
+# S4 method for class 'PHGDataSet'
+plotHaploDist(object, drop = FALSE)
+
+ +
+

Arguments

+ + +
object
+

a PHGDataSet object

+ + +
...
+

Additional arguments, for use in specific methods

+ + +
drop
+

Do you want unused unique count bins to be plotted? Defaults to TRUE.

+ +
+ +
+ + +
+ + + + + + + diff --git a/reference/port.html b/reference/port.html index 8516462..d39ff87 100644 --- a/reference/port.html +++ b/reference/port.html @@ -7,7 +7,7 @@ rPHG2 - 0.5 + 0.6