rmskFilter: Filter transposable elements from rmsk reference based on...

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

Filter transposable elements from rmsk reference based on given their gene, family, and class ID.

Description

For filtering out the select transposable elements from gene, family, and class to down-stream analysis, we provide this function to help quickly list all options out. You can run this function first setting show to TRUE to see every possibility. Then you provide a character vector including the name of family/class you want to select. The function will then return a subset of the rmsk dataframe.

Usage

rmskFilter(rmskInfo, gene = NULL, family = NULL, class = NULL, show = FALSE)

Arguments

rmskInfo	rmsk dataframe, with three columns, gene_id, family_id, and class_id
gene	a vector including the gene names you want
family	a vector including the family names you want
class	a vector including the class names you want
show	if you want to first see all possible family/class, set this as TRUE

Value

a subset of rmsk dataframe including three columns, gene, family and class

Examples

data(hg19rmsk_info)
df <- hg19rmsk_info

#list all possibilities
rmskFilter(df, show=TRUE)

# select family
rmskFilter(df, family="hAT-Charlie")

# select class
df_subset <- rmskFilter(df, class= c("LINE", "SINE"))

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