gsrc: Genome Structure Rearrangement Calling in Genomes with High Synteny
Version 1.1

Pipeline to read and analyze raw SNP array data. The data is preprocessed and normalized. Genotypes and CNVs are called. Synteny blocks are calculated and translocations detected. The results can be plotted with special functions.

Browse man pages Browse package API and functions Browse package files

AuthorFabian Grandke [cre, aut], Birgit Samans [aut]
Date of publication2016-10-17 12:41:19
MaintainerFabian Grandke <grafabian@gmail.com>
LicenseGPL-3
Version1.1
URL http://github.com/grafab/gsrc
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("gsrc")

Man pages

call_geno: Genotype with kmeans using three clusters
check_raw: Check raw data
cnv: Copy Number Variation
filter_cnv: Filter Copy number variations
filt_samp: Filter Samples
filt_snps: Filter SNPs
find_blocks: Find Synteny Blocks
find_peak: Find peaks
geno_baf_rratio: Genotype with kmeans using three clusters
intens_theta: Preprocess raw values and calculate Intensity and Theta...
interpol: Interpolate cluster means
plot_cnv: Plot Copy Number Variations
plot_global: Plot all chromosomes of a population
plot_gsr: Plot all chromosomes of a sample
plot_raw_snp: Plot raw SNP
plot_samp: Plot all chromosomes of a sample
plot_trans_locations: Plot translocations
read_intensities: Read multiple idat files.
read_sample_sheets: Read sample sheet(s)
remove_suffix: Remove suffix from sample names
rename_samples: Rename sample names
require_package: Require package wrapper
segm: Segmentation of R ratio values
split_sb: Split synteny blocks
synteny_info: Class for synteny information
trans_location: Find translocations

Functions

call_geno Man page Source code
check_raw Man page Source code
cnv Man page Source code
filt_samp Man page Source code
filt_snps Man page Source code
filt_snps.norm_data Man page Source code
filt_snps.raw_data Man page Source code
filter_cnv Man page Source code
find_blocks Man page Source code
find_peak Man page Source code
geno_baf_rratio Man page Source code
intens_theta Man page Source code
interpol Man page Source code
plot_cnv Man page Source code
plot_global Man page Source code
plot_gsr Man page Source code
plot_raw_snp Man page Source code
plot_samp Man page Source code
plot_trans_locations Man page Source code
read_intensities Man page Source code
read_sample_sheets Man page Source code
remove_suffix Man page Source code
rename_samples Man page Source code
rename_samples.norm_data Man page Source code
rename_samples.raw_data Man page Source code
require_package Man page Source code
segm Man page Source code
split_sb Man page Source code
synteny_info Man page
trans_location Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/synteny.R
inst/doc/introduction.R
inst/doc/synteny.html
inst/doc/introduction.html
inst/doc/introduction.Rmd
inst/doc/synteny.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test_segm.R
tests/testthat/test_filt_samp.R
tests/testthat/test_cnv.R
tests/testthat/read_intensities.R
tests/testthat/test_check_raw.R
tests/testthat/test_geno_rratio_baf.R
tests/testthat/test_filt_snps.R
tests/testthat/test_intens_theta.R
NAMESPACE
NEWS
R
R/synteny.R
R/preprocess.R
R/plot.R
R/raw.R
R/filter.R
R/tools.R
R/process.R
vignettes
vignettes/brassica_synteny_filtered.rda
vignettes/introduction_files
vignettes/introduction_files/figure-html
vignettes/introduction_files/figure-html/unnamed-chunk-22-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-20-3.png
vignettes/introduction_files/figure-html/unnamed-chunk-17-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-32-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-14-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-28-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-12-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-29-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-31-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-21-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-23-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-17-2.png
vignettes/introduction_files/figure-html/unnamed-chunk-18-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-30-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-33-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-20-2.png
vignettes/introduction_files/figure-html/unnamed-chunk-25-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-20-1.png
vignettes/cotton_synteny_filtered.rda
vignettes/introduction_cache
vignettes/introduction_cache/html
vignettes/introduction_cache/html/unnamed-chunk-31_7d400f8476971a879c0ec0e5feb79517.rdx
vignettes/introduction_cache/html/unnamed-chunk-31_7d400f8476971a879c0ec0e5feb79517.RData
vignettes/introduction_cache/html/unnamed-chunk-31_7d400f8476971a879c0ec0e5feb79517.rdb
vignettes/introduction_cache/html/__packages
vignettes/introduction.Rmd
vignettes/synteny.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/read_sample_sheets.Rd
man/check_raw.Rd
man/filt_snps.Rd
man/plot_global.Rd
man/plot_gsr.Rd
man/find_peak.Rd
man/filter_cnv.Rd
man/read_intensities.Rd
man/require_package.Rd
man/geno_baf_rratio.Rd
man/call_geno.Rd
man/remove_suffix.Rd
man/trans_location.Rd
man/plot_cnv.Rd
man/synteny_info.Rd
man/segm.Rd
man/interpol.Rd
man/plot_samp.Rd
man/plot_trans_locations.Rd
man/plot_raw_snp.Rd
man/split_sb.Rd
man/cnv.Rd
man/rename_samples.Rd
man/find_blocks.Rd
man/filt_samp.Rd
man/intens_theta.Rd
gsrc documentation built on May 20, 2017, 2 a.m.