callrate: Calculates call rate as proportion of called SNPs in the...

In Meiomap/SureTypeSCR: Library for (single-cell) SNP array processing

Description

Calculate call rate as proportion of called SNPs in the input dataframe.

Usage

callrate(.data)

Arguments

.data

data frame from scbasic or compatible

Value

Table with call rate(s) of the input data frame.

Examples

setwd(system.file(package='SureTypeSCR'))

samplesheet=system.file('files/GSE19247_example.csv',package='SureTypeSCR')
manifest=system.file('files/HumanCytoSNP-12v2_H.bpm',package='SureTypeSCR')
cluster=system.file('files/HumanCytoSNP-12v2_H.egt',package='SureTypeSCR')

##Load data
df=scbasic(manifest,cluster,samplesheet)

##Get overall callrate
#df %>% callrate() 

##Get callrate per individual
#df %>% 
# group_by(individual) %>% 
# callrate()

##Get callrate as allelic fractions and pivot to columns
#df %>% 
# group_by(individual,gtype) %>% 
# callrate() %>% 
# pivot_wider(names_from=gtype,values_from=Callrate)

Meiomap/SureTypeSCR documentation built on Dec. 17, 2021, 3:22 a.m.