exportPrimers {TAPseq} | R Documentation |
A set of functions for TAP-seq primer export. Convert primers stored in
TsIO
or TsIOList
objects to
a simple data.frame
for easier export. Or create BED format tracks for
primers and write them to files for viewing in a genome browser (e.g. IGV).
createPrimerTrack(object, color = 1) ## S4 method for signature 'TsIO' createPrimerTrack(object, color = 1) ## S4 method for signature 'TsIOList' createPrimerTrack(object, color = 1) exportPrimerTrack(..., con) primerDataFrame(object) ## S4 method for signature 'TsIO' primerDataFrame(object) ## S4 method for signature 'TsIOList' primerDataFrame(object)
object |
|
color |
Color used for the track (Default: black). Can be any of the three kinds of R color specifications. |
... |
One or more primer BED tracks created by
|
con |
Connection to which tracks are written. Typically a .bed file. |
For createPrimerTrack
a data.frame
with the primer track in
BED format.
createPrimerTrack,TsIO-method
: Create primer BED track from TsIO
objects
createPrimerTrack,TsIOList-method
: Create primer BED track from TsIOList
objects
exportPrimerTrack
: Export primer BED tracks files
primerDataFrame,TsIO-method
: Create a data.frame
with primer data from TsIO
primerDataFrame,TsIOList-method
: Create a data.frame
with primer data from TsIOList
# chr11 primers example data data("chr11_primers") # pick best primers based on predicted off-targets best_primers <- pickPrimers(chr11_primers, n = 1, by = "off_targets") # primers data can be exported to a simple data.frame to e.g. write them to a .csv file primers_df <- primerDataFrame(best_primers) head(primers_df) # primer binding sites in transcript sequences can be converted to genomic coordinates to create # a BED track to visualize primers in a genome browser (e.g. IGV) # create primer BED track with a fancy color track <- createPrimerTrack(best_primers[1:5], color = "steelblue3") # tracks can be written to .bed files using a little helper function (replace con = "" by a file) exportPrimerTrack(track, con = "") ## Not run: # one can easily export primer tracks for multiple TsIO or TsIOList objects (e.g. inner and # outer nested primers) to one .bed file using different colors for each object. see vignette for # a practical example: vignette("tapseq_primer_design", package = "TAPseq") obj1 <- best_primers[1:5] obj2 <- best_primers[6:10] exportPrimerTrack(createPrimerTrack(obj1, color = "steelblue3"), createPrimerTrack(obj2, color = "goldenrod1"), con = "path/to/file.bed") ## End(Not run)