I have chopped my dataset based on chromosomes and for some, getRS function never stops when imput = T. Debugging showed that the failing function is convertNA, where the condition of while loop is never false.

library('CNTools')
combined.seg = read.csv('https://www.dropbox.com/s/c97sodr709ixl8z/combined.seg.csv?raw=1', h = T)

chr16.seg = combined.seg[combined.seg$chrom == "16", ];
chr16.cn = CNSeg(chr16.seg)
chr16.rd = getRS(chr16.cn, by = "region", what = "median") # works fine

chr18.seg = combined.seg[combined.seg$chrom == "18", ];
chr18.cn = CNSeg(chr18.seg)
chr18.rd = getRS(chr18.cn, by = "region", what = "median", imput = F) # works fine again

chr18.seg = combined.seg[combined.seg$chrom == "18", ];
chr18.cn = CNSeg(chr18.seg)
chr18.rd = getRS(chr18.cn, by = "region", what = "median", imput = T) # runs forever