annotateTarget | R Documentation |
wrapper around segmentAnnotate
, used to
annotate the target set by a column in the query set. See
Details for required input formats.
annotateTarget(
query,
target,
qcol = colnames(query),
tcol,
prefix,
details = FALSE,
only.best = TRUE,
sort = TRUE,
minJaccard,
collapse = TRUE,
msgfile = stdout()
)
query |
the query set of segments (genomic intervals) |
target |
the target set of segments (genomic intervals) |
qcol |
column names to copy from target to it's best match in query, defaults to all columns |
tcol |
column names of target to include in the returned table, defaults to none |
prefix |
column name prefix for the copied columns |
details |
set to |
only.best |
only consider the top-ranking query hit |
sort |
sort hits by rank |
minJaccard |
minimal Jaccard index (intersect/union) threshold;
overlaps below this value will NOT be reported; NOTE that this will
set argument |
collapse |
if |
msgfile |
file pointer for progress messages and warnings, defaults to stdout, useful when using in context of command line pipes |
Wrapper around segmentAnnotate
, used to
annotate the target set by a column in the query set. Note that
coordinates must already be ‘indexed’, see ?segmentAnnotate
and ?coor2index
. The default options (only.best=TRUE
,
collapse=TRUE
yield a result matrix with 1 row for each
target
(nrow(results)==nrow(target)
, annotated by
only the best ranking overlapping query
segment(s), ie. the
the query
segment(s) with the highest Jaccard index. If multiple
query
segments have the same Jaccard index, they are collapsed
into ;-separated lists. If collapse=FALSE
, each overlapping
query
segment will have its own row, and the result matrix
is longer (nrow(results)>=nrow(target)
). If only.best=FALSE
,
all overlapping query
segments will be reported, and optionally
sorted by rank (sort
).
Additionaly a minimal Jaccard filter can be applied
(option minJaccard
), and only query
segments with a
higher Jaccard index are reported.
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