Description Usage Arguments Value Warning Author(s) References See Also Examples
The function extracts positions of standard peaks from an ABIF file and calculates the sizes of products in specified channels.
1 2 3 4 5 6 7 8 9 10 | sizeCaller(x_abifile,
rsizes = r_sizes,
ranges = matrix(rep(c(2.3, 8), sum(npeaks.per.channel)), nrow = sum(npeaks.per.channel), byrow = TRUE),
ranges.bp,
thres_start = 2,
channels = 1:4,
npeaks.per.channel = rep(1, length(channels)),
locus.names = paste(rep("V", length(channels)), 1:sum(npeaks.per.channel), sep = ""),
strain.name = deparse(substitute(x_abifile)),
...)
|
x_abifile |
list generated by |
rsizes |
sizes of reference peaks in basepairs. peaks not to be counted are given as NA. |
ranges |
matrix of time ranges across which peaks are looked for in channels specified
in |
ranges.bp |
matrix of basepair ranges across which peaks are looked for in channels specified
in |
thres_start |
threshhold, below which peaks are looked for (see function |
channels |
channel numbers containing products of unknown sizes |
npeaks.per.channel |
array containing number of peaks per channel (defaults to one peak per channel) |
locus.names |
array of locus names |
strain.name |
name of strain to be analyzed |
... |
arguments passed on to |
matrix returning the peak sizes in basepairs of each locus
Warnings are issued if sizes in one or several loci cannot be calculated or if
searchStandardPeaks
is unable to extract the standard ladder from
x_abifile
.
Johannes Elias
package seqinr
by Charif, D. and Lobry, J.R. (2007)
1 2 | # returns the sizes of peaks in the standard ABIF file
sizeCaller(r_abif)
|
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