rachelss / rrelrates

rrelrates

Produce relative rates on from trees using the reltime method of Tamura et al. 2012.

This package is a work in progress. Currently it is limited to primates and data available in ensembl. You can install the package via devtools

devtools::install_github("rachelss/rrelrates")

You must also install the following dependencies:

devtools::install_github("dwinter/rensembl")
source("http://bioconductor.org/biocLite.R")
biocLite(c("GO.db", "biomaRt"))

Examples

Mean and Variance of the relative rates

geneinfo("CCND1")
#> [1] "CCND1"

#> $CCND1_ENSPPYP00000003434_Pabe
#> [1] 2.232375
#> 
#> $mean
#> [1] 0.9768734
#> 
#> $var
#> [1] 0.3532899

rrelrates's Issues

Import from, rather than depend on, other packages

It seems travis is grumpy about how many other packages this one depends on 😄

The solution (which cleaner anyway) is to import specific functions from other pcakages. So, in DESCRIPTION the packages go under Imports.

Then, for any function you want to use from, say, GO.db you add the line

#'@importFrom GO.db function_I_want_to_use

When you run devtools::document() the functions get added to NAMESPACE.

error in pi_around_gene in caroline.r

when length(snp_ids) > 1000

Error in as.vector(x, "character") :
cannot coerce type 'externalptr' to vector of type 'character'