ampliconReport {RSeqMeth} | R Documentation |
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
ampliconReport(fnames = NA, minMass = 1500, maxMass = 7000)
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. |
Fragmentation is analyzed for both the C and T Cleavage reactions.
No value returned - reports generated are written to the directory the sequence files are read from.
Aaron Statham
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.
## 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"))