Find point-to-range overlaps

Question

I have a dataframe df1:

df1 <- read.table(text=\" Chr06  79641   
Chr06   82862   
Chr06   387314  
Chr06   656098  
Chr06   678491  
Chr06   1018696\", heade         


        

Answer 1

Here is a data.table solution as an alternative to GenomicRanges:

library(data.table)
dt1 <- data.table(df1)[, V3 := V2]
dt2 <- data.table(df2, key = c("V2", "V3"))
foverlaps(dt1, dt2)[V1 == i.V1][, -c(4, 6), with = F]
#       V1      V2      V3    i.V3
# 1: Chr06   79720   87043   82862
# 2: Chr06  387314  387371  387314
# 3: Chr06 1018676 1018736 1018696