README.md

In roszenil/CCDBcurator: Chromosome Count Database curator

CCDB Tutorial

author: Rosana Zenil-Ferguson date: October 27, 2018

1. Download chromosome number records from CCDB

First you will have to download a dataset from CCDB and use chromer before hand.

Download your dataset at http://ccdb.tau.ac.il/

You can use package chromer from Matt Pennell to download datasets from https://github.com/ropensci/chromer

install.packages(chromer)

library(chromer)
anemia.counts <- chrom_counts(taxa="Anemia", rank="genus")

2. Curating all my records and accessing all curated records (Oct 2018)

There are possible tens of thousands of patterns that appear in CCDB records. As much as (one-womanly) possible, I have integrated the most common regular expressions. However, you should expect some errors still in CCDBcurator please report them using open issue in GitHub (github.com/roszenil/CCDBcurator)

Load the library of CCDB curator

install_github("roszenil/CCDBcurator")
library("CCDBcurator")
anemia.cleancounts<-CCDBcurator(anemia.counts)
anemia.cleancounts

Access all the records in angiosperms and ferns cleaned available in October 2018 using the data() function

data(angiorecordsclean2018)
data(fernrecordsclean2018)

Acess all the records in angiosperms and ferns by genus available in October 2018

data(angiocsomefulltable)
angiocsomefulltable$Physalis # All chromosome numbers for Physalis

data(ferncsomefulltable)
ferncsomefulltable$Anemia # All chromosome numbers for Anemia

3. Curating a gametophytic chromosome number

You can clean a single gametophytic entry from CCDB using the function gametophytic.translator(). This function will create a table with 5 columns 1.Genus= Genus name, 2.Species= Species name (format usable to match with phylogenies) 3.CountTranslation (numeric)= A numeric vector with the counts ready to use for analyses 4.Type= Gametophytic 5. CountOriginal= The original record in CCDB. This is done to control for errors.

Example 1

gametophytic.translator(anemia.counts[1,])

4. Curating a sporophytic chromosome number

You can clean a single gametophytic entry from CCDB using the function sporophytic.translator(). This function will create a table with 5 columns 1.Genus= Genus name, 2.Species= Species name (format usable to match with phylogenies) 3.CountTranslation (numeric)= A numeric vector with the counts ready to use for analyses 4.Type= Gametophytic 5. CountOriginal= The original record in CCDB. This is done to control for errors.

Example 2

sporophytic.translator(anemia..counts[2,])

roszenil/CCDBcurator documentation built on May 27, 2019, 11:41 p.m.