addAnno {XCIR} | R Documentation |
Read a given annotation file and merge it with a data.table containing the relevant information to estimate inactivated X chromosome expression and filter out SNPs with low coverage.
addAnno(dt, seqm_annotate = TRUE, read_count_cutoff = 20, het_cutoff = 3, filter_pool_cutoff = 3, anno_file = NULL)
dt |
A |
seqm_annotate |
A |
read_count_cutoff |
A |
het_cutoff |
A |
filter_pool_cutoff |
A |
anno_file |
A |
If the samples all have the same genotype (e.g: technical replicates),
filter_pool_cutoff
will sum counts across samples and preserve SNPs
that pass the cutoff on both the reference and alternate alleles. This
may lead to samples with 0 counts on either allele but will prevent removing
heterozygous sites with lower coverage (especialliy in skewed samples).
seqm_anno
will call annotatePlain
from the seqminer
package. For convenience, seqminer
's necessary annotation sources can
be copied into XCIR
's extdata folder. See ?annotatePlain for more
information.
A data.table
object that contains allelic coverage, genotype
and annotations at the covered SNPs.
annotatePlain
# 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)