R: Calculate number of Estimated Unique Counts (EUC's)...
k2n_calc
R 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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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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
>