Input files available for gwasurvivr vignette?
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dec986 • 0
@dec986-9652
Last seen 19 months ago

Hello,

I'm reading through the vignette on the gwasurvivr R package http://bioconductor.org/packages/devel/bioc/vignettes/gwasurvivr/inst/doc/gwasurvivr_Introduction.html

but I'm finding it not so useful without the specified input files, i.e.

michiganCoxSurv(vcf.file=vcf.file,
                covariate.file=pheno.file,
                id.column="ID_2",
                sample.ids=sample.ids,
                time.to.event="time",
                event="event",
                covariates=c("age", "SexFemale", "DrugTxYes"),
                inter.term=NULL,
                print.covs="only",
                out.file="michigan_only",
                r2.filter=0.3,
                maf.filter=0.005,
                chunk.size=100,
                verbose=TRUE,
                clusterObj=NULL)

I would really appreciate if someone could tell me where I could find sample input files for these.

This command is just an example, there are lots of input files there, and I can only make guesses when they show the table through head and so on.

gwasurvivr • 121 views
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@james-w-macdonald-5106
Last seen 15 hours ago
United States

Right before the section that you supply in your post is this section:

vcf.file <- system.file(package="gwasurvivr",
                        "extdata", 
                        "michigan.chr14.dose.vcf.gz")
pheno.fl <- system.file(package="gwasurvivr",
                        "extdata", 
                        "simulated_pheno.txt")
pheno.file <- read.table(pheno.fl,
                         sep=" ", 
                         header=TRUE,
                         stringsAsFactors = FALSE)
head(pheno.file)

Which seems to provide all the things you think are not provided?

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I didn't understand that system.file refers to files that were downloaded with the package

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