README.md

In ellisztamas/snaptools: Tools for analysing data from the snapdragon hybrid zone

snaptools

Tools for analysing data from the snapdragon hybrid zone in the collada de Toses.

snaptools provides tools for running common operations on data from the Antirrhinum majus hybrid zone project. The aim is to provide functions for some specific tasks that multiple people might want to implement, to avoid replication of effort and creeping errors.

Basic functions

• categorise_flower_scores uses scores for red and yellow pigmentation to infer flower colour phenotype, and genotypes for Rosea and Sulfurea.

• match_ramet: David Field and Harald Ringbauer went through the Antspec and genotype data to check inconsistencies and identify plants that had been tagged and genotypes more than once. Where duplicates are found, they were grouped as a unique genotype (a genet) with a label PlantID_Final. Names of any duplicates are given in the column RametID, which is a string of undetermined length that is difficult to parse. match_ramet is an efficient way to look for PlantIDs that could be in either PlantID_Final or RametID. Usage is the same as the base R function match; see ?match for details and caveats with this approach.

• density_frequency uses GPS information data to define the density of plants around a set of focal plants. See ?density_frequency for details of how density is calculated. If phenotype categories are given, it also returns the phenotypic frequency of the focal plants as the density of neighbours of the same phenotype divided by the density of all neighbours.

• lgc2faps: Convert a dataframe from the table of strings we get from LGC to a data.frame of integers. Output format can be imported into FAPS directly for paternity analysis.

• dgennorm: Calculate the PDF of the generalised normal distribution.

• vectorise_locus: Convert a vector of raw data from LGC into a vector of inetegers.

Installation

snaptools can be installed from with R straight from GitHub using devtools.

devtools::install_github("ellisztamas/snaptools")

If you don't have devtools installed, install it with install.packages('devtools').

Then you can import the package just like any other R package with:

library("snaptools")

This will also import the documentation for each function, which is the best place to go to find out what functions are doing. For example, to see what the function to calculate density and frequency is doing, run

library("snaptools")
`?density_frequency

or

?snaptools::density_frequency

Dependencies

None

Author

Tom Ellis ([e-mail])

ellisztamas/snaptools documentation built on May 19, 2020, 2:03 p.m.