Description Usage Arguments Author(s) See Also Examples
This function calculates the number of required flows for a concrete amplicon panel.
1 2 | flowsPanel(bed.table, genom, order.flows = c("T", "A", "C", "G"),
ret.seq = FALSE)
|
bed.table |
A data frame corresponding to a BED file, which can be read into R with the function |
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. |
Michael Bockmayr and Jan Budczies
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ### 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)
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