inst/testScripts/complete/VUMC/71.doQDNASeq.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

#!/usr/bin/env Rscript

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library("aroma.seq");

dataSet <- "AlbertsonD_2012-SCC";
organism <- "Homo_sapiens";

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# Setup
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path <- file.path("annotationData", "organisms", organism);
filename <- "human_g1k_v37.fasta";
fa <- FastaReferenceFile(filename, path=path);
print(fa);

# Data set
path <- file.path("fastqData", dataSet, organism);
ds <- IlluminaFastqDataSet$byPath(path);
print(ds);

# Process at most three FASTQ files
ds <- extract(ds, 1:min(3, length(ds)));

# In addition to SAM read group data inferred from the Illumina FASTQ
# files, manual set the library information for the whole data set.
setSamReadGroup(ds, SamReadGroup(LB="MPS-034"));


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Complete QDNAseq pipeline
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cns <- doQDNAseq(ds, reference=fa, binWidth=1000, verbose=-20);
print(cns);


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# HISTORY:
# 2013-07-11
# o Created from 21.BwaAlignment.R.
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