call_gd1: Genetic Distance 1
In acm4r: Align-and-Count Method comparisons of RFLP data
Description
Usage
Arguments
Value
Note
Author(s)
References
Examples
Description
Genetic Distance 1 which includes a lambda parameter
Usage
1
call_gd1(intable, gcrit = 5, lambda = 0.05)
Arguments
intable
is the name of the acm table.
gcrit
is the threshold of genetic distance such
that two lanes are matching if and only if the genetic
distance between them is less than gcrit. Is used to get
a list of ids for subjects who have gd distance less than
gcrit
lambda
is the minimum number of bands that need to
match
Value
A matrix with two colums of fingerprint IDs. Each line
represents a match according to gcrit.
Note
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
#matching by GD1
res_gd1<-call_gd1(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
Genetic Distance 1 which includes a lambda parameter
Usage
1 | call_gd1(intable, gcrit = 5, lambda = 0.05)
|
Arguments
intable |
is the name of the acm table. |
gcrit |
is the threshold of genetic distance such that two lanes are matching if and only if the genetic distance between them is less than gcrit. Is used to get a list of ids for subjects who have gd distance less than gcrit |
lambda |
is the minimum number of bands that need to match |
Value
A matrix with two colums of fingerprint IDs. Each line
represents a match according to gcrit.
Note
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 | #matching by GD1
res_gd1<-call_gd1(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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