General Information

File: <%=x@filename%>
Type: FASTA
Sequence Length Range: <%=sl.range[1]%> to <%=sl.range[2]%> bases
Total Sequences: <%=sum(x@seq.lengths)%>
Unique Sequences: <%=length(x@hash)%>

Nucleotide Frequency by Position

<% basePlot(x) ggsave(file.path(dir, 'images', 'basefreqs.png'), width=WIDTH, height=HEIGHT, dpi=DPI) %>

Nucleotide Proportion by Position

<% basePlot(x, type="proportion") + geom_hline(yintercept=0.25, color="purple") ggsave(file.path(dir, 'images', 'baseprops.png'), width=WIDTH, height=HEIGHT, dpi=DPI) %>

N Frequency by Position

<% basePlot(x, bases='N') ggsave(file.path(dir, 'images', 'nfreq.png'), width=WIDTH, height=HEIGHT, dpi=DPI) %>

GC Content by Position

<% gcPlot(x) ggsave(file.path(dir, 'images', 'gc.png'), width=WIDTH, height=HEIGHT, dpi=DPI) %>

Sequence Length Distribution

<% seqlenPlot(x) ggsave(file.path(dir, 'images', 'seqlengths.png'), width=WIDTH, height=HEIGHT, dpi=DPI) %>

Most Frequent Sequences

<% if (x@hashed) { x <- makeHashTable(x) print(x, type="html") } else { cat("No sequence frequency information available - readSeqFile() run with hash=FALSE") } %>
Report produced by the Bioconductor package qrqc
(c) Vince Buffalo 2011-2012, License: GPL 2.0