twice

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

library(twice)

## Warning: replacing previous import 'flextable::rotate' by 'ggpubr::rotate' when
## loading 'twice'

## Warning: replacing previous import 'flextable::font' by 'ggpubr::font' when
## loading 'twice'

## Warning: replacing previous import 'flextable::border' by 'ggpubr::border' when
## loading '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)