poorBisulfiteConversion | R Documentation |
Use bedfile with positons of Cs that are in non-methylated context to obtain stats about the number of informative Cs and conversion status of Cs per read
poorBisulfiteConversion( bamFile, genomeFile, bedFileC, bedFileG, regionGR, samtoolsPath = "" )
bamFile |
String with path to bam file with alignments of reads to genome |
genomeFile |
String with path to fasta file with genome sequence |
bedFileC |
String with path to .bed file with locations of Cs to be evaluated (for forward strand calls) |
bedFileG |
String with path to .bed file with locations of Gs to be evaluated (for reverse strand calls) |
regionGR |
Genomic range of region for which to extract reads. It can also be a string denoting the region, e.g. "X:8069396-8069886" |
samtoolsPath |
Path to samtools executable (default="") if not in unix $PATH |
A data frame with the names of the reads, the count of the number of informative Cs per region (not NAs), the maximum number of possible Cs in the regon, and the fraction of the informative Cs which have been bisulfite converted
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.