Nothing
## ----setup,include=FALSE------------------------------------------------------
knitr::opts_chunk$set( echo = TRUE )
library( Haplin, quietly = TRUE )
## -----------------------------------------------------------------------------
dir.exmpl <- system.file( "extdata", package = "Haplin" )
exemplary.file1 <- paste0( dir.exmpl, "/HAPLIN.trialdata.txt" )
my.gen.data.haplin <- genDataRead( file.in = exemplary.file1, file.out = "trial_data1",
dir.out = ".", format = "haplin", n.vars = 0 )
exemplary.file3 <- paste0( dir.exmpl, "/exmpl_data.ped" )
my.gen.data <- genDataRead( exemplary.file3, file.out = "ped_data", dir.out = ".",
format = "ped" )
## ----eval=FALSE---------------------------------------------------------------
# ?genDataRead
#
# example( genDataRead )
## ----add_cov_data_read--------------------------------------------------------
add.cov.file <- paste0( dir.exmpl, "/add_cov_data2.dat" )
my.gen.data.haplin3 <- genDataRead( file.in = exemplary.file1, file.out = "trial_data3",
dir.out = ".", format = "haplin", n.vars = 0, cov.file.in = add.cov.file )
my.gen.data.haplin3
add.cov.file2 <- paste0( dir.exmpl, "/add_cov_data.dat" )
my.gen.data2 <- genDataRead( exemplary.file3, file.out = "ped_data2", dir.out = ".",
format = "ped", cov.file.in = add.cov.file2 )
my.gen.data2
## ----show_summary-------------------------------------------------------------
my.gen.data
## ----showPheno_demo-----------------------------------------------------------
# by default - showing first 5 entries:
showPheno( my.gen.data )
# getting all the info:
head( showPheno( my.gen.data, n = "all" ), n = 20 )
showPheno( my.gen.data, from = 4, to = 15 )
# show information about females only:
head( showPheno( my.gen.data, sex = 2, n = "all" ), n = 20 )
## ----showPheno_demo2----------------------------------------------------------
females.pheno <- showPheno( my.gen.data, sex = 2 )
head( females.pheno )
## ----nindiv_demo--------------------------------------------------------------
nindiv( my.gen.data )
nfam( my.gen.data )
## ----nsnps--------------------------------------------------------------------
nsnps( my.gen.data )
## ----showSNPnames-------------------------------------------------------------
showSNPnames( my.gen.data ) # by default - showing only first 5 SNPs
showSNPnames( my.gen.data, from = 12, to = 31 )
## ----showGen_demo-------------------------------------------------------------
showGen( my.gen.data, markers = c( 10,15,121 ) ) # by default - showing first 5 entries
showGen( my.gen.data, from = 31, to = 231 )
## ----showGen_demo2------------------------------------------------------------
subset.genes <- showGen( my.gen.data, from = 31, to = 231, markers = c( 10,15,121 ) )
subset.genes
## ----eval=FALSE---------------------------------------------------------------
# my.prepared.gen.data <- genDataPreprocess( data.in = my.gen.data, map.file =
# "my_gen_data.map", design = "triad", file.out = "my_prepared_gen_data",
# dir.out = "." )
## ----eval=FALSE---------------------------------------------------------------
# gen.data.subset <- genDataGetPart( data.in = my.gen.data, markers = c( 3:15,22 ),
# design = "triad", file.out = "my_gen_data_subset", dir.out = "." )
## ----eval=FALSE---------------------------------------------------------------
# my.prepared.gen.data <- genDataLoad( filename = "my_prepared_gen_data",
# dir.in = "." )
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