Description Usage Arguments Details Value See Also Examples
Reads allele database from file, or loads database provided with likeLTD.
1 | load.allele.database(path=NULL, kit=NULL)
|
path |
Path to the database file, or |
kit |
Only used if |
If not NULL, then the input should consist of a file in the following format:
Marker | Allele | LUS | BP | EA1 | EA2 | ... |
TH01 | 5 | 5 | 166 | 1 | 2 | |
TH01 | 6 | 6 | 170 | 212 | 44 | |
TH01 | 8 | 8 | 178 | 90 | 69 | |
TH01 | 8.3 | 5 | 181 | 0 | 0 | |
TH01 | 10 | 10 | 186 | 7 | 6 | |
TH01 | R/-100 | NA | NA | 0 | 0 | |
vWA | 13 | 7.3 | 163 | 0 | 5 | |
vWA | 14 | 7.5 | 167 | 86 | 24 | |
... | ||||||
The first line needs to be present. The first column indicated the locus, the
second the name of the allele, the third the longest uninterrupted sequence of the allele,
the fourth the fragment length. The next columns
are the frequencies for specific ethnic groups. There are no limits to the
number of ethnic groups included. If the name of an allele is
R
for the discrete model, or -100
for the peak heights model, then it is ignored.
If running the discrete model, LUS values are not used, so may be provided as NA
.
A table, as read from the file.
read.unc.profile, read.known.profiles
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## Not run:
# datapath to example files
datapath = file.path(system.file("extdata", package="likeLTD"),"hammer")
# File paths and case name for allele report
admin = pack.admin.input(
cspFile = file.path(datapath, 'hammer-CSP.csv'),
refFile = file.path(datapath, 'hammer-reference.csv'),
caseName = "hammer",
kit= "SGMplus"
)
# get allele database
load.allele.database(kit=admin$kit)
## End(Not run)
|
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