ionflows (version 1.1)

flowsPanel: Simulation algorithm to calculate the number of required flows for a sequence panel in BED format.

Description

This function calculates the number of required flows for a concrete amplicon panel.

Usage

flowsPanel(bed.table, genom, order.flows = c("T", "A", "C", "G"),  ret.seq = FALSE)

Arguments

bed.table

A data frame corresponding to a BED file, which can be read into R with the function readBed.

genom

Genome to be used to extract the sequences. It should be in the BSgenome class. The genome corresponding to the UCSC hg19 build can be obtained from the package BSgenome.Hsapiens.UCSC.hg19 .

order.flows

Character vector indicating the order of the nucleotides used to synthesize the complementary strand during semiconductor sequencing.

ret.seq

logical. If 'TRUE', a matrix containing the sequences extracted from the input BED file and the corresponding forward and backward flow sequence constructed during semiconductor sequencing is returned.

See Also

readBed

Examples

### Load the BED file using the readBed function or use the example dataset:

data(chp2,package="ionflows")

### Load the BSgenome from which the genomic sequences of the amplicons in
### the BED file are to be extracted from, for example the BSgenome.Hsapiens.UCSC.hg19
### package for the UCSC hg19 build, which should be priorly installed .

## Not run: library(BSgenome.Hsapiens.UCSC.hg19)

### Run flowsPanel

## Not run: flowsPanel(chp2,BSgenome.Hsapiens.UCSC.hg19)

### A BED file can also be directly loaded into R:

## Not run: dset <- readBed("path/to/bed")
## Not run: flowsPanel(dset,genom)