correct_oversaturation: Correcting EUC of oversaturated fragments.

In RNAprobR: An R package for analysis of massive parallel sequencing based RNA structure probing data

Description

If for a given fragment the number of observed unique barcodes is equal to the total barcode complexity (all combinations of barcodes are associated with a given fragment), then the readsamples function assignes infinite EUC. This can be corrected by the function correct_oversaturation(). By comparing observed read counts with EUCs for other fragments it calculates the correction factor. Then, for the oversaturated fragments it multiplies the observed read counts by the correction factor to estimate EUC. The assumption behind this correction is that fragments have similar rate of PCR duplicates production.

Usage

correct_oversaturation(euc_GR, read_counts_file)

Arguments

euc_GR	GRanges produced by readsamples() function
read_counts_file	path to a file with observed read counts.

Value

euc_GR GRanges analogous to the readsamples() function output, but with finite EUCs where infinity was present.

Examples

write(c("DummyRNA\t1\t2\t1000", "DummyRNA\t3\t4\t1024"),
     file="dummy_unique_barcode")
write(c("DummyRNA\t1\t2\t5000", "DummyRNA\t3\t4\t10000"),
      file="dummy_read_counts")
my_EUCs <- readsamples(samples = "dummy_unique_barcode", euc = "Fu", m=1024)
correct_oversaturation(euc_GR = my_EUCs,
                       read_counts_file = "dummy_read_counts")

RNAprobR documentation built on Nov. 8, 2020, 5:57 p.m.