1、vcfR
BiocManager::install('vcfR')
library('vcfR')
library(pinfsc50)
library(reshape2)
library(ggplot2)
vcf <- system.file('extdata','pinf_sc50.vcf.gz',package = 'pinfsc50')
vcf <- vcfR::read.vcfR(vcf, verbose = FALSE)
dp <- extract.gt(vcf, element='DP', as.numeric = TRUE)
str(vcf)
dpf <- melt(dp, varnames=c('Index', 'Sample'),value.name = 'Depth', na.rm=TRUE)
p <- ggplot(dpf, aes(x=Sample, y=Depth)) +geom_violin(fill='#C0C0C0', adjust=1.0,scale = 'count', trim=TRUE)
p <- p + theme_bw()
p <- p + ylab('Read Depth (DP)')
p <- p + theme(axis.title.x = element_blank(),axis.text.x = element_text(angle = 60, hjust = 1))
p <- p + stat_summary(fun.data=mean_sdl,geom='pointrange', color='black')
p <- p + scale_y_continuous(trans=scales::log2_trans(),)
breaks=c(1, 10, 100, 1000)
p
heatmap.bp(dp[501:1500,], rlabels = FALSE)
dna_file <- system.file('extdata','pinf_sc50.fasta',package = 'pinfsc50')
gff_file <- system.file('extdata','pinf_sc50.gff',package = 'pinfsc50')
dna <- ape::read.dna(dna_file, format = 'fasta')
gff <- read.table(gff_file, sep='\t',quote='')
chrom <- create.chromR(name='Supercontig',vcf=vcf, seq=dna,ann=gff)
chrom <- masker(chrom, min_QUAL=0, min_DP=350,max_DP=650, min_MQ=59.5,max_MQ=60.5)
chrom <- proc.chromR(chrom)
chromoqc(chrom, dp.alpha=20)
