General Information
File: <%=obj@filename%>
Type: FASTA
Sequence Length Range: <%=sl.range[1]%> to
<%=sl.range[2]%> bases
Total Sequences: <%=sum(obj@seq.lengths)%>
Unique Sequences: <%=length(obj@hash)%>
Nucleotide Frequency by Position
<%
png(file.path(dir, 'images', 'basefreqs.png'), width=WIDTH, height=HEIGHT)
plotBases(obj)
dev.off()
%>
Nucleotide Proportion by Position
<%
png(file.path(dir, 'images', 'baseprops.png'), width=WIDTH, height=HEIGHT)
plotBases(obj, type="prop")
dev.off()
%>
N Frequency by Position
<%
png(file.path(dir, 'images', 'nfreq.png'), width=WIDTH, height=HEIGHT)
plotBases(obj, bases='N')
dev.off()
%>
GC Content by Position
<%
png(file.path(dir, 'images', 'gc.png'), width=WIDTH, height=HEIGHT)
plotGC(obj)
dev.off()
%>
Sequence Length Distribution
<%
png(file.path(dir, 'images', 'seqlengths.png'), width=WIDTH, height=HEIGHT)
plotSeqLengths(obj)
dev.off()
%>
Most Frequent Sequences
<%
if (obj@hashed) {
x <- makeHashTable(obj)
print(x, type="html")
} else {
cat("No sequence frequency information available - readSeqFile() run with hash=FALSE")
}
%>
Report produced by the R package qrqc