dnamatch

Description

dnaimport is a function for importing text-files from the lab-software into structure for further processing.

Usage

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dnamatch(fn, freqfile, reffold = NULL, TAptrn, SIDpat, BIDpat, Thist = 1,
  Tnew = 1, threshLR = 1000, threshHeight = 10, threshStutt = 0.1,
  threshMaj = 0.6, pD = 0, pC = 0, sameKL = FALSE, N = 5000)

Arguments

fn

A folder with stain files. Full directory must be given.

freqfile

A file containing population frequencies for alleles. Full directory must be given.

reffold

A folder with stored personal references. Default is no references. Full directory must be given.

TAptrn

Filename structure of samples to evaluate. For instance TAptrn="TA-".

SIDpat

Pattern of name which is sample ID (SID_BID_CID)=("-S0001_BES00001-14_2014234231"). Here SIDpat="-S". Can also be a vector.

BIDpat

Pattern of name which is unique for all samples to evaluate. (SID_BID_CID)=("-S0001_BES00001-14_2014234231"). Here BIDpat="_BES".

Thist

Number of days back in time for file to be imported(stains). Samples older than Tnew are declared as OLD.

Tnew

Number of days back in time which are defined as NEW files. If today is 2014-11-16, Tnew=3 means that files from 2014-11-13 are declared as NEW.

threshLR

Threshold for extracting a match to file.

threshHeight

Acceptable peak height (rfu) in stains.

threshStutt

Acceptable stutter ratio in stains (relative peak heights) .

threshMaj

If second largest allele has ratio (relative to the largest allele) above this threshold, then second allele is part of the major profile (used for extracting major from mixture). If the relative peak height between second and third largest allele has ratio greater than this threshold, no major is assigned.

pD

Assumed drop-out rate per marker (parameter in LR model).

pC

Assumed drop-in rate per marker (parameter in LR model).

sameKL

Boolean whether matches within same case ID number are shown.

N

Database size used for estimating population frequencies. Used to assign new allele frequenceis.

Details

dnamatch imports case-stains from Genemapper/Siris automaticly and feeds it into a structure for doing comparison matching. Note: Samplenames must have this format: "SID_BID_CID". The samplename must be unique and consist of SID=Sample ID, BID=Unique ID for all samples, CID=Case ID.

Timestamp="YY-MM-DD-HH-MM-SS" is used as identification key of when the dnamatch function was run. Match results are stored as a table in matchfile.csv with the timestamp. Matches which are earlier found in matchfile.csv will not be stored again. The column "Checked" can be used for comments. More details about a given dnamatch run are stored in the folder "session" with corresponding timestamp.

Author(s)

Oyvind Bleka <Oyvind.Bleka.at.fhi.no>

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