readsamples: Import of tables prepared by Galaxy workflow to R environment

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

Description

Function readsamples() reads the output of read processing and mapping workflow which has to consist of 4 columns 1) RNAid, 2)Insert start, 3)Insert end, 4)Unique barcode count. It combines separate files coming from the same treatment (e.g. controls) and calculates estimated unique counts (EUCs) by either (a) keeping unique counts (euc="counts"), (b) using formula from Fu GK et al. PNAS 2011 (binomial distribution calculation) (euc="Fu") or (c) using method described in Kielpinski and Vinther, NAR 2014 (euc="HRF-Seq") If euc="Fu" then the count of all possible barcodes is required (m), e.g. if you use 7 nucleotide, fully degenerate random barcodes (NNNNNNN) then m=16384 (m=4**7) If euc="HRF-Seq" then the path to a precomputed k2n file is required (generate using k2n_calc() function)(default: "counts")

Usage

readsamples(samples, euc = "counts", m = "", k2n_files = "")

Arguments

samples	vector with paths to unique_barcodes files to be combined
euc	method of calculating estimated unique counts (default: "counts")
m	random barcode complexity (required if and only if euc="Fu")
k2n_files	vector with paths to k2n files corresponding to files given in samples (required if and only if euc="HRF-Seq"; order important!). Recycled if necessary

Value

euc_GR GRanges containing information: 1) seqnames (sequence name; RNAid) 2) Start, 3) End, 4) EUC value of a given fragment

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

References

Fu, G.K., Hu, J., Wang, P.H., and Fodor, S.P. (2011). Counting individual DNA molecules by the stochastic attachment of diverse labels. Proc Natl Acad Sci U S A 108, 9026-9031. Kielpinski, L.J., and Vinther, J. (2014). Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res.

See Also

comp, plotReads, k2n_calc

Examples

write("DummyRNA\t1\t2\t3",file="dummy_unique_barcode")
readsamples(samples = "dummy_unique_barcode", euc = "counts")

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