In ferygood/twice: A collections of useful functions to analyze transcription factors and transposable elements data

In this vignette, I will explained how to use each functions with examples.

library(twice)

ensIDtoName() function can convert ensembl ID to common gene name. This function is useful when you want to obtain information more easily than reading ensembl ID.

# load data
data(hmchimpGene)
data(hmKZNFs337)
# filter row names only include KZNFs
dfKZNFs <- 
    hmchimpGene[rownames(hmchimpGene) %in% hmKZNFs337$ensembl_gene_id, ]
df <- ensIDtoName(dfKZNFs, "hsapiens")

saveTErmsk() extract gene/family/class information of transposable elements from repeatmasker annotation gtf file.

#teAnnot <- saveTErmsk(rmskGTF, fileName=FALSE)

ferygood/twice documentation built on May 4, 2023, 11:26 p.m.