plot_ma: Create MA plot per individual.

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

Description

Plot XY plot of logarithmic difference (M) and logarithmic average (A) of intensity signals-

Usage

plot_ma(.data,norm=TRUE,smooth=FALSE,nocalls=FALSE,n=1)

Arguments

.data	data frame returned by scbasic or a compatible function
norm	boolean flag indicating whether to use normalized (TRUE) or raw (FALSE) intensities
smooth	boolean flag indicating whether to apply smoothing spline per genotype (AA/BB/AB) cluster (TRUE or FALSE, set to FALSE by default.
nocalls	boolean flag indicating whether to plot SNPs that did not call (TRUE or FALSE, set to FALSE by default.
n	fraction of data to use from .data (real number in range 0..1)

, set to 1 by default meaning all points will by plotted.

Value

ggplot object with MA plots facetted by individual

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)

#Visualise MA plot
#df %>% plot_ma(norm=TRUE,n=0.1)

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