#' get de novo data from Fromer et al. schizophrenia exome study
#'
#' De novo mutation data sourced from Supplementary table 1:
#' Fromer et al. (2014) Nature 506:179-184
#' doi: 10.1038/nature12929
#'
#' @export
#'
#' @return data frame of de novos, including gene symbol, functional consequence
#' (VEP format), chromosome, nucleotide position and SNV or INDEL type
fromer_de_novos <- function() {
url = "http://www.nature.com/nature/journal/v506/n7487/extref/nature12929-s2.xlsx"
variants = gdata::read.xls(url, stringsAsFactors=FALSE)
variants$temp = strsplit(variants$Locus, ":")
variants$chrom = sapply(variants$temp, "[", 1)
variants$chrom = gsub("chr", "", variants$chrom)
variants$start_pos = sapply(variants$temp, "[", 2)
variants$end_pos = variants$start_pos
# fix indel ranges
indels = grepl("\\.\\.", variants$start_pos)
variants$start_pos[indels] = sapply(strsplit(variants$start_pos[indels], "\\.\\."), "[", 1)
variants$end_pos[indels] = sapply(strsplit(variants$end_pos[indels], "\\.\\."), "[", 2)
variants$ref_allele = variants$Reference.allele
variants$alt_allele = variants$Alternate.allele
vep = apply(variants, 1, get_vep_consequence, verbose=TRUE)
variants$consequence = sapply(vep, "[", 1)
variants$hgnc = sapply(vep, "[", 2)
variants$person_id = variants$Proband.ID
variants$study_code = "fromer_nature_2014"
variants$publication_doi = "10.1038/nature12929"
variants$study_phenotype = "schizophrenia"
# get the sex for each variant
variants$sex = variants$Proband.gender
variants = subset(variants, select=c("person_id", "sex", "chrom", "start_pos",
"end_pos", "ref_allele", "alt_allele", "hgnc", "consequence",
"study_code", "publication_doi", "study_phenotype"))
return(variants)
}
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