ampliconReport {RSeqMeth}R Documentation

Generate report files

Description

Specified sequence files are read and reports generated.

Sequence files must be plaintext - no header. Whitespace is allowed.

Four files are generated:

<SEQUENCE NAME> T/C Report.csv - analysis of the CpG containing fragments

<SEQUENCE NAME> T/C Spectra.pdf - illustration of the predicted spectra

Usage

ampliconReport(fnames = NA, minMass = 1500, maxMass = 7000)

Arguments

fnames A character vector of file names of sequences to be analyzed. If left to default, files are chosen interactively.
minMass The minimal mass of a peak to be included in the analysis.
maxMass The maximal mass of a peak to be included in the analysis.

Details

Fragmentation is analyzed for both the C and T Cleavage reactions.

Value

No value returned - reports generated are written to the directory the sequence files are read from.

Author(s)

Aaron Statham

References

Coolen MW, Statham AL, Gardiner-Garden M, Clark SJ. (2007) Nucleic Acids Research 35(18):e119 Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

See Also

analyzeSequenom

Examples

## choose sequence files interactively
#ampliconReport()

## generate report files from EN1.txt and SCTR.txt in the current working directory
#ampliconReport(c("EN1.txt", "SCTR.txt"))

[Package RSeqMeth version 1.0.2 Index]