Course of work with molecular data in R 2015

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Since academic year 2015/16 is the course scheduled in SIS as MB120C16.

R is nowadays probably the most powerful tool for statistics of all types. There are plenty of modules available for work with molecular data. Those will be introduced during the course. Previous knowledge of R is useful, but not necessary. Course will be taught from January 14 to 16, 2015 from 9 AM to about 5 PM at the Department of Botany, Faculty of Science, Charles University in Prague in classroom "Krajinova posluchárna" (B14, 2nd mezzanine on the end of the corridor; Wednesday and Thursday) and in classroom "posluchárna OŽP" (B12, 1st mezzanine on the end of the corridor on right side; Friday).

Presentation with test data is available

List of topics

  • Basic work in R -- how to enter commands, install packages, read help, types of variables, indexes, etc.
  • Bioconductor
  • Load and export molecular data of various types and formats.
  • Mikrosatellites, AFLP, SNP, sequences
  • Download molecular data from on-line databases
  • Extractions of SNP from sequencing data
  • Extraction of polymorphism from sequences
  • Distance matrices, import of custom matrices
  • Manipulations with data, conversions among formats
  • Basic statistics, genetic indices heterozygosity, HWE, F-statistics
  • Export of figures
  • Phylogenetic trees (NJ, UPGMA, ML) and display and test
  • PCoA
  • MSN
  • DAPC
  • Whole genome SNP data
  • Spatial analysis -- Mantel test, Moran's I, Monmonier, sPCA
  • Basic map creation
  • Structure
  • Alignments
  • Manipulations with trees, work with big sets of trees
  • Phylogenetic independent contrast
  • Phylogenetic autocorrelation
  • Phylogenetic PCA
  • Ancestral state reconstruction

Used packages: Geneland, PBSmapping, ParallelStructure, RandomFields, RgoogleMaps, TeachingDemos, XML, ade4, adegenet, adephylo, akima, ape, colorspace, combinat, corrplot, fields, gplots, grid, ips, lattice, mapdata, mapproj, maps, maptools, muscle, pegas, permute, phangorn, phyloch, phytools, poppr, rworldmap, seqinr, sp, spam, tcltk, vegan.

The course will be in English.

For course you need

  • Working Wi-Fi. Eduroam or in application form You can ask for temporary password.
  • Installed R. I also recommend to install some graphical user interface like RStudio, RKWard, R commander or some similar according to your choice.

In case of any questions, wishes, comments just ask! Using comment form below, by mail or so on.

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