call_erra: Error Analysis for 1D Electrophoresis Gels

In acm4r: Align-and-Count Method comparisons of RFLP data

Description

This function analyzes fingerprint replicate data. Replicates are repeated measurements of the same sample in one or more gels, which allows the reproducibility of the measurement to be ascertained.

Usage

call_erra(rep.file, work_dir = ".", dnum = 1, sd = 4, delete = FALSE)

Arguments

rep.file	is the full name and path of the replicate file
work_dir	is where the datasets should be stored
dnum	is the file number
sd	is the standard deviation needed to calculate all things, Salamon et al. (1998) suggested a value of 4 for sd
delete	logical value indicating if you want to delete any pre-existing acm.par files. Default is FALSE

Value

the parameter filed called acm.par, needed by call_acm. This file contains information on about the measurement error present in the data.

Note

call_erra doesn't work for unequal number of trials. This function needs to be run before call_acm.

Author(s)

Andrea Benedetti [e-mail]

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

#generate the error parameter file needed by call_acm
call_erra("replicates.in",  dnum=1, sd=1, delete=TRUE)

acm4r documentation built on May 1, 2019, 7:50 p.m.