gsrc: Genome Structure Rearrangement Calling in Genomes with High Synteny

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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.

Author
Fabian Grandke [cre, aut], Birgit Samans [aut]
Date of publication
2016-10-17 12:41:19
Maintainer
Fabian Grandke <grafabian@gmail.com>
License
GPL-3
Version
1.1
URLs

View on CRAN

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

Files in this package

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