inst/DerivedData/README.md

In byandell/DOread: Read DO data

title: "Derived Data for R/doqtl2" author: "Brian S Yandell" date: "June 12, 2016" output: html_document

These files are for converting the DOQTL data (or rather, that curated by Karl Broman with R/qtl2 packages) for use with the R/doqtl2 package. There are some conversions and some new files.

• convertRDS.Rmd: convert DOQTL RData and CSV to RDS
• vcf_snp_2db.R: (re)create cc_foundersnps.sqlite (update of R/0_vcf2db.R)
• vcf_indel_2db.R: create cc_founderindels.sqlite (new)
• svs.Rmd: create svs8_*.rds files (new)

The derived data go into a folder called DerivedData. This is in a hard-wired folder that is, for now, machine specific. On my laptop it is:

dirpath <- file.path("~/Documents/Research/attie_alan/DO", "data")
datapath <- file.path(dirpath, "DerivedData")

The files in this derived_data folder have this hard-wired. The only other place where it is hard-wired is for the shiny server, which is in inst/shiny/setup.R. These will have to be changed for local installation. It would be nice to have this in only one place. Next iteration.

RDS Files

RDS files are apparently an improvement on RData files. They hold one R object and are the same size, but are quicker to use. See for instance R bloggers.

SQLite Files

I modified the SNP SQLite code to include consequence and Ensembl IDs. The InDel SQLite code is a minor change to get indels. Note that there is a column labelled allele, which is the name used in creation of the VCF, but this is pretty close to the column alleles, which we use in DOQTL stuff.

SVS Files

These are in a different format. Look carefully at this. Not totally happy, but it works.

byandell/DOread documentation built on May 13, 2019, 9:26 a.m.