Nothing
## -----------------------------------------------------------------------------
library(EthSEQ)
## Run the analysis
ethseq.Analysis(
target.vcf = system.file("extdata", "Samples.HGDP.10000SNPs.vcf",package="EthSEQ"),
model.gds = system.file("extdata", "Reference.Gencode.Exome.10000SNPs.gds",package="EthSEQ"),
out.dir = file.path(tempdir(),"EthSEQ_Analysis/"),
verbose=TRUE,
cores =1,
composite.model.call.rate = 1,
space = "3D")
## Load and display computed ethnicity annotations
ethseq.annotations = read.delim(file.path(tempdir(),"EthSEQ_Analysis/Report.txt"),
sep="\t",as.is=TRUE,header=TRUE)
head(ethseq.annotations)
## Delete analysis folder
unlink(file.path(tempdir(),"EthSEQ_Analysis/"),recursive=TRUE)
## ----eval=FALSE---------------------------------------------------------------
# library(EthSEQ)
#
# ## View all available reference models
# getModelsList()
#
# ## Run the analysis
# ethseq.Analysis(
# target.vcf = system.file("extdata", "Samples.HGDP.10000SNPs.vcf",package="EthSEQ"),
# model.available = "Gencode.Exome",
# model.assembly = "hg38",
# model.pop = "All",
# out.dir = file.path(tempdir(),"EthSEQ_Analysis/"),
# verbose=TRUE,
# cores =1,
# composite.model.call.rate = 1,
# space = "3D")
#
# ## Delete analysis folder
# unlink(file.path(tempdir(),"EthSEQ_Analysis/"),recursive=TRUE)
## ----eval=FALSE---------------------------------------------------------------
# library(EthSEQ)
#
# ## Download BAM file used in the analysis
# download.file("https://github.com/cibiobcg/EthSEQ_Data/raw/master/BAM/HGDP00228.sub_GRCh38.bam",
# destfile = file.path(tempdir(),"HGDP00228.sub_GRCh38.bam"))
# download.file("https://github.com/cibiobcg/EthSEQ_Data/raw/master/BAM/HGDP00228.sub_GRCh38.bam.bai",
# destfile = file.path(tempdir(),"HGDP00228.sub_GRCh38.bam.bai"))
# download.file("https://github.com/cibiobcg/EthSEQ_Data/raw/master/BAM/HGDP01200.sub_GRCh38.bam",
# destfile = file.path(tempdir(),"HGDP01200.sub_GRCh38.bam"))
# download.file("https://github.com/cibiobcg/EthSEQ_Data/raw/master/BAM/HGDP01200.sub_GRCh38.bam.bai",
# destfile = file.path(tempdir(),"HGDP01200.sub_GRCh38.bam.bai"))
# download.file("https://github.com/cibiobcg/EthSEQ_Data/raw/master/BAM/HGDP01201.sub_GRCh38.bam",
# destfile = file.path(tempdir(),"HGDP01201.sub_GRCh38.bam"))
# download.file("https://github.com/cibiobcg/EthSEQ_Data/raw/master/BAM/HGDP01201.sub_GRCh38.bam.bai",
# destfile = file.path(tempdir(),"HGDP01201.sub_GRCh38.bam.bai"))
#
# ## Create BAM files list
# write(c(file.path(tempdir(),"HGDP00228.sub_GRCh38.bam"),
# file.path(tempdir(),"HGDP01200.sub_GRCh38.bam"),
# file.path(tempdir(),"HGDP01201.sub_GRCh38.bam")),
# file.path(tempdir(),"BAMs_List.txt"))
#
# ## Run the analysis
# ethseq.Analysis(
# bam.list = file.path(tempdir(),"BAMs_List.txt"),
# model.available = "Gencode.Exome",
# out.dir = file.path(tempdir(),"EthSEQ_Analysis/"),
# verbose = TRUE,
# cores = 1,
# aseq.path = file.path(tempdir(),"EthSEQ_Analysis/"),
# run.genotype = TRUE,
# mbq = 20,
# mrq = 20,
# mdc = 10,
# composite.model.call.rate = 1,
# space = "3D",
# bam.chr.encoding = TRUE) # chromosome names encoded without "chr" prefix in BAM files
#
# ## Delete analysis folder
# unlink(file.path(tempdir(),"EthSEQ_Analysis/"),recursive=TRUE)
## ----eval=FALSE---------------------------------------------------------------
# library(EthSEQ)
#
# ## Create multi-step refinement matrix
# m = matrix("",ncol=2,nrow=2)
# m[1,1] = "EUR|AFR|AMR"
# m[2,2] = "EUR|AMR"
#
# ## Run the analysis on a toy example with only 10000 SNPs
# ethseq.Analysis(
# target.vcf = system.file("extdata","Samples.HGDP.10000SNPs.vcf",package="EthSEQ"),
# out.dir = file.path(tempdir(),"EthSEQ_Analysis/"),
# model.available = "Gencode.Exome",
# verbose = TRUE,
# refinement.analysis = m,
# composite.model.call.rate = 1,
# space = "3D")
#
# ## Delete analysis folder
# unlink(file.path(tempdir(),"EthSEQ_Analysis/"),recursive=TRUE)
## ----eval=FALSE---------------------------------------------------------------
# library(EthSEQ)
#
# ### Load list of VCF files paths
# vcf.files = c(system.file("extdata","RefSample1.vcf", package="EthSEQ"),
# system.file("extdata","RefSample2.vcf", package="EthSEQ"))
#
# ### Load samples annotations
# annot.samples = read.delim(system.file("extdata","Annotations_Test_v3.txt",package="EthSEQ"))
#
# ### Create reference model
# ethseq.RM(
# vcf.fn = vcf.files,
# annotations = annot.samples,
# out.dir = file.path(tempdir(),"EthSEQ_Analysis/"),
# model.name = "Reference.Model",
# bed.fn = NA,
# call.rate = 1,
# cores = 1)
#
# ## Delete example file
# unlink(file.path(tempdir(),"EthSEQ_Analysis/"),recursive=TRUE)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.