Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup, echo=FALSE--------------------------------------------------------
library(BinaryDosage)
## ---- eval = T, echo = T, message = F, warning = F, tidy = T------------------
gen3bchrfile <- system.file("extdata", "set3b.chr.imp", package = "BinaryDosage")
sample3bfile <- system.file("extdata", "set3b.sample", package = "BinaryDosage")
bdfile3b_chr <- tempfile()
gentobd(genfiles = c(gen3bchrfile, sample3bfile), bdfiles = bdfile3b_chr)
bdinfo3b_chr <- getbdinfo(bdfiles = bdfile3b_chr)
## ---- eval = T, echo = T, message = F, warning = F, tidy = T------------------
gen1bfile <- system.file("extdata", "set1b.imp", package = "BinaryDosage")
bdfile1b <- tempfile()
gentobd(genfiles = gen1bfile,
bdfiles = bdfile1b,
snpcolumns = c(1L, 3L, 2L, 4L, 5L),
header = TRUE)
bdinfo1b <- getbdinfo(bdfiles = bdfile1b)
## ---- eval = T, echo = T, message = F, warning = F, tidy = T------------------
gen3bfile <- system.file("extdata", "set3b.imp", package = "BinaryDosage")
sample3bfile <- system.file("extdata", "set3b.sample", package = "BinaryDosage")
bdfile3b <- tempfile()
gentobd(genfiles = c(gen3bfile, sample3bfile),
bdfiles = bdfile3b,
snpcolumns = c(0L,2L:5L))
bdinfo3b <- getbdinfo(bdfiles = bdfile3b)
## ---- eval = T, echo = T, message = F, warning = F, tidy = T------------------
gen4bfile <- system.file("extdata", "set4b.imp", package = "BinaryDosage")
sample4bfile <- system.file("extdata", "set4b.sample", package = "BinaryDosage")
bdfile4b <- tempfile()
gentobd(genfiles = c(gen4bfile, sample4bfile),
bdfiles = bdfile4b,
snpcolumns = c(1L,2L,4L,5L,6L),
startcolumn = 7L,
impformat = 2L)
bdinfo4b <- getbdinfo(bdfiles = bdfile4b)
## ---- eval = T, echo = T, message = F, warning = F, tidy = T------------------
gen2bfile <- system.file("extdata", "set2b.imp", package = "BinaryDosage")
sample2bfile <- system.file("extdata", "set2b.sample", package = "BinaryDosage")
bdfile2b <- tempfile()
gentobd(genfiles = c(gen2bfile, sample2bfile),
bdfiles = bdfile2b,
snpcolumns = c(1L,3L,2L,4L,5L),
impformat = 1L)
bdinfo2b <- getbdinfo(bdfiles = bdfile2b)
## ---- eval = T, echo = T, message = F, warning = F, tidy = T------------------
gen3bfile <- system.file("extdata", "set3b.imp", package = "BinaryDosage")
sample3bfile <- system.file("extdata", "set3b.sample", package = "BinaryDosage")
bdfile3bm1 <- tempfile()
gentobd(genfiles = c(gen3bfile, sample3bfile),
bdfiles = bdfile3bm1,
snpcolumns = c(-1L,2L:5L),
chromosome = "1")
bdinfo3bm1 <- getbdinfo(bdfiles = bdfile3bm1)
## ---- eval = T, echo = T, message = F, warning = F, tidy = T------------------
gen3bfile <- system.file("extdata", "set3b.imp", package = "BinaryDosage")
sample3bnhfile <- system.file("extdata", "set3bnh.sample", package = "BinaryDosage")
bdfile3bnh <- tempfile()
gentobd(genfiles = c(gen3bfile, sample3bnhfile),
bdfiles = bdfile3bnh,
snpcolumns = c(0L,2L:5L),
header = c(FALSE, FALSE))
bdinfo3bnh <- getbdinfo(bdfiles = bdfile3bnh)
## ---- eval = T, echo = T, message = F, warning = F, tidy = T------------------
gen4bgzfile <- system.file("extdata", "set4b.imp.gz", package = "BinaryDosage")
sample4bfile <- system.file("extdata", "set4b.sample", package = "BinaryDosage")
bdfile4bgz <- tempfile()
gentobd(genfiles = c(gen4bgzfile, sample4bfile),
bdfiles = bdfile4bgz,
snpcolumns = c(1L,2L,4L,5L,6L),
startcolumn = 7L,
impformat = 2L,
gz = TRUE)
bdinfo4bgz <- getbdinfo(bdfiles = bdfile4bgz)
## ---- eval = T, echo = T, message = F, warning = F, tidy = T------------------
gen3bchrfile <- system.file("extdata", "set3b.chr.imp", package = "BinaryDosage")
sample3bfile <- system.file("extdata", "set3b.sample", package = "BinaryDosage")
geninfo <- getgeninfo(genfiles = c(gen3bchrfile, sample3bfile), index = TRUE)
aaf <- unlist(genapply(geninfo = geninfo, getaaf))
altallelefreq <- data.frame(SNP = geninfo$snps$snpid, aafcalc = aaf)
knitr::kable(altallelefreq, caption = "Calculated aaf", digits = 3)
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