call_bablbs: BABLBS (Band Added Band Lost Band Substituted)
In acm4r: Align-and-Count Method comparisons of RFLP data
Description
Usage
Arguments
Value
Note
Author(s)
References
Examples
Description
BABLBS clustering means that two fingerprints match if they
differ only through a lost band, a gained band, or a
substituted band
Usage
1
call_bablbs(intable, minmatch = 2)
Arguments
intable
is the name of the acm table.
minmatch
is the threshold of band number such that
two lanes are matching if and only if the number of
matching bands between them is more than minmatch.
Value
a matrix of 2 columns where each row represents a pair of
matching lanes.
Note
call_bablbs doesn't work for minmatch<5
Pass the result of this function to and pass this result to
clusters to synthesize the results
Author(s)
Andrea Benedetti andrea.benedetti@mcgill.ca
Sahir Rai Bhatnagar
XiaoFei Zhao
References
Salamon et. al (1998) Accommodating Error Analysis in
Comparison and Clustering of Molecular Fingerprints.
Emerging Infectious Diseases Vol. 4, No. 2, April-June 1998
Abasci LLC. JAMES v1.0 User Documentation. 2002.
Examples
1
2
3
#bablbs, GD1, and GD2 all work with the results from call_acm
#now check matching by bablbs
res_bab<-call_bablbs(res1)
acm4r documentation built on May 1, 2019, 7:50 p.m.
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Description Usage Arguments Value Note Author(s) References Examples
Description
BABLBS clustering means that two fingerprints match if they differ only through a lost band, a gained band, or a substituted band
Usage
1 | call_bablbs(intable, minmatch = 2)
|
Arguments
intable |
is the name of the acm table. |
minmatch |
is the threshold of band number such that two lanes are matching if and only if the number of matching bands between them is more than minmatch. |
Value
a matrix of 2 columns where each row represents a pair of matching lanes.
Note
call_bablbs doesn't work for minmatch<5
Pass the result of this function to and pass this result to
clusters to synthesize the results
Author(s)
Andrea Benedetti andrea.benedetti@mcgill.ca
Sahir Rai Bhatnagar
XiaoFei Zhao
References
Salamon et. al (1998) Accommodating Error Analysis in Comparison and Clustering of Molecular Fingerprints. Emerging Infectious Diseases Vol. 4, No. 2, April-June 1998
Abasci LLC. JAMES v1.0 User Documentation. 2002.
Examples
1 2 3 | #bablbs, GD1, and GD2 all work with the results from call_acm
#now check matching by bablbs
res_bab<-call_bablbs(res1)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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