Read SNPs from RNA-Seq that have not been phased.
For phased samples, use
data.table of allele specific read counts.
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# Example workflow for documentation vcff <- system.file("extdata/AD_example.vcf", package = "XCIR") # Reading functions vcf <- readRNASNPs(vcff) vcf <- readVCF4(vcff) # Annotation functions # Using seqminer (requires additional annotation files) anno <- addAnno(vcf) # Using biomaRt anno <- annotateX(vcf) # Do not remove SNPs with 0 count on minor allele anno0 <- annotateX(vcf, het_cutoff = 0) # Summarise read counts per gene # Assuming data is phased, reads can be summed across genes. genic <- getGenicDP(anno, highest_expr = FALSE) # Unphased data, select SNP with highest overall expression. genic <- getGenicDP(anno, highest_expr = TRUE)
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