vcfR-method: show

In vcfR: Manipulate and Visualize VCF Data

show

Description

Display a summary of a vcfR object.

head returns the first parts of an object of class vcfR.

The brackets ('[]') subset objects of class vcfR

The plot method visualizes objects of class vcfR

Usage

## S4 method for signature 'vcfR'
show(object)

## S4 method for signature 'vcfR'
head(x, n = 6, maxchar = 80)

## S4 method for signature 'vcfR,ANY,ANY,ANY'
x[i, j, samples = NULL, ..., drop]

## S4 method for signature 'vcfR'
plot(x, y, ...)

## S4 method for signature 'vcfR,missing'
rbind2(x, y, ...)

## S4 method for signature 'vcfR,ANY'
rbind2(x, y, ...)

## S4 method for signature 'vcfR,vcfR'
rbind2(x, y, ...)

## S4 method for signature 'vcfR'
dim(x)

## S4 method for signature 'vcfR'
nrow(x)

Arguments

object	a vcfR object
x	object of class vcfR
n	number of rows to print
maxchar	maximum number of characters to print per line
i	vector of rows (variants) to include
j	vector of columns (samples) to include
samples	vector (numeric, character or logical) specifying samples, see details
...	arguments to be passed to other methods
drop	delete the dimensions of an array which only has one level
y	not used

Details

The method show is used to display an object. Because vcf data are relatively large, this has been abbreviated. Here we display the first four lines of the meta section, and truncate them to no more than 80 characters. The first eight columns and six rows of the fix section are also displayed.

The method head is similar to show, but is more flexible. The number of rows displayed is parameterized by the variable n. And the maximum number of characters to print per line (row) is also parameterized. In contract to show, head includes a summary of the gt portion of the vcfR object.

The square brackets ([]) are used to subset objects of class vcfR. Rows are subset by providing a vector i to specify which rows to use. The columns in the fix slot will not be subset by j. The parameter j is a vector used to subset the columns of the gt slot. Note that it is essential to include the first column here (FORMAT) or downsream processes will encounter trouble.

The samples parameter allows another way to select samples. Because the first column of the gt section is the FORMAT column you typically need to include that column and sample numbers therefore begin at two. Use of the samples parameter allows you to select columns by a vector of numerics, logicals or characters. When numerics are used the samples can be selected starting at one. The function will then add one to this vector and include one to select the desired samples and the FORMAT column. When a vector of characters is used it should contain the desired sample names. The function will add the FORMAT column if it is not the first element. When a vector of logicals is used a TRUE will be added to the vector to ensure the FORMAT column is selected. Note that specification of samples will override specification of j.

The plot method generates a histogram from data found in the 'QUAL' column from the 'fix' slot.

vcfR documentation built on Feb. 16, 2023, 8:12 p.m.