Last data update: 2014.03.03

R: Calculate number of Estimated Unique Counts (EUC's)...
k2n_calcR Documentation

Calculate number of Estimated Unique Counts (EUC's) corresponding to given number of observed unique barcodes.

Description

Function calculates EUC's for each number of observed barcodes accounting for differential ligation probability of different barcodes. Function k2n_calc() writes file with a vector in which an i-th element is an estimated unique count given observing i unique barcodes.

Usage

k2n_calc(merged_file, unique_barcode_file, output_file)

Arguments

merged_file

path to merged_temp file containing 4 column: 1) RNAid, 2) Start, 3) End, 4) Barcode sequence (required)

unique_barcode_file

character with path to unique_barcode file (required)

output_file

name of a file to be generated (if specified [recommended] function will write a file, if not - function will return a vector)

Value

If output_file specified function writes a file, if not - returns a vector.

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

References

Kielpinski, L.J., and Vinther, J. (2014). Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res.

See Also

readsamples

Examples

write(c("DummyRNA\t1\t1\tA", "DummyRNA\t1\t1\tC", "DummyRNA\t2\t2\tG",
        "DummyRNA\t2\t2\tT"),file="dummy_merged_file")
write(c("DummyRNA\t1\t1\t2", "DummyRNA\t2\t2\t2"),
        file="dummy_unique_barcode")
k2n_calc(merged_file = "dummy_merged_file",
        unique_barcode_file = "dummy_unique_barcode")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(RNAprobR)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: plyr

Attaching package: 'plyr'

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAprobR/k2n_calc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: k2n_calc
> ### Title: Calculate number of Estimated Unique Counts (EUC's)
> ###   corresponding to given number of observed unique barcodes.
> ### Aliases: k2n_calc
> 
> ### ** Examples
> 
> write(c("DummyRNA\t1\t1\tA", "DummyRNA\t1\t1\tC", "DummyRNA\t2\t2\tG",
+         "DummyRNA\t2\t2\tT"),file="dummy_merged_file")
> write(c("DummyRNA\t1\t1\t2", "DummyRNA\t2\t2\t2"),
+         file="dummy_unique_barcode")
> k2n_calc(merged_file = "dummy_merged_file",
+         unique_barcode_file = "dummy_unique_barcode")
[1] 1 2
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>