Simple plot of an allelic ladder from ABIF data
Simple representation of an observed allelic ladder.
plotladder(abifdata, chanel, calibr, allele.names = "identifiler", npeak = NULL, ...)
abifdata |
the result returned by |
chanel |
the dye number |
calibr |
a mandatory calibration function to convert time into bp |
allele.names |
name of the dataset which contains allele names as in |
npeak |
expected number of peaks, deduced from |
... |
arguments forwarded to |
Returns invisibly the location of peaks in bp.
J.R. Lobry
citation("seqinr")
# # load an example of allelic ladder results from an ABIF (*.fsa) file: # data(ECH) # # Extract from internal size standard chanel number 5 the location # of 14 peaks: # ECH.maxis <- peakabif(ECH, 5, npeak = 14, tmin = 2.7, thres = 0.1, fig = FALSE)$maxis # # Load data about the expected size of peaks in bp for calibration: # data(gs500liz) lizbp <- gs500liz$liz # All peaks size in bp lizbp[!gs500liz$mask1 | !gs500liz$mask2] <- NA # Mark useless peaks lizbp <- lizbp[-c(1,2)] # The first two peaks are not extracted from ECH ECH.calibr <- splinefun(ECH.maxis[!is.na(lizbp)], lizbp[!is.na(lizbp)]) # # Show the allelic ladder for the 4 dyes: # plotladder(ECH, 1, ECH.calibr, tmin = 3.1, thres = 0.3, fig = FALSE) plotladder(ECH, 2, ECH.calibr, tmin = 3.1, thres = 0.35, fig = FALSE) plotladder(ECH, 3, ECH.calibr, tmin = 3.1, thres = 0.2, fig = FALSE) plotladder(ECH, 4, ECH.calibr, tmin = 3.1, thres = 0.2, fig = FALSE)
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