Align-and-Count Method comparisons of RFLP data

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Description

Fragment lengths or molecular weights from pairs of lanes are compared, and a number of matching bands are calculated using the Align-and-Count Method. Band intensities are not used in this method.This version of acm will perform all distinct pairwise comparisons between lanes. The first lane will be compared to all following lanes. The second lane will be compared to the third, fourth, etc..

Usage

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call_acm(input, work_dir = ".", dnum = 1)

Arguments

input

The input file format for fragment and lane information are as the file example.in shows. Each line (record) should define a band. The file must be sorted so that the bands from a lane are together; the file must be sorted by unique lane identifier (ULI). There must be three fields (separated by white space – that is, seperated by any combination of spaces and tabs). The first field must be the ULI. The second field is the gel image identifier (GII). This is only critical for the first fragment read in for the lane; for subsequent fragments, the second field must simply be present. ULI and GII names must not contain any spaces; I strongly suggest that these fields contain only letters, numbers, and underscore characters. The third field should contain the fragment length or molecular weight data for the fragment. Lines that cannot be parsed into these three fields will be recored in acm.log. Check acm.log after each run to see the number of lanes read in and to check for lines from the input file that could not be parsed. Lines must be no longer than 199 characters.

work_dir

This is where the work is being done

dnum

is the file number

Value

The output from acm or acmone gives a comparison of two lanes on each line of output in the form: ULI ULI numbands numbands num_matches The first field is identifier for the first lane in the comparison. The third field is the number of bands read in for this first lane. The second field is the identifier for the second lane in the comparison. The fourth field is the number of band read in for this second lane. The fifth field is the number of fragments found to match between the two lanes. The number of matches found may be different depending on whether the lanes came from the same gel image or from different gel images (see the file acm.par).

Note

Requires a parameter file generated by call_erra

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

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#perform the basic pairwise comparison via the align and count algorithm
res1<-call_acm("experiments.in")