plotAlongChrom2 {tilingArray} | R Documentation |
Plot the results of segmentation along a chromosomal region
plotAlongChrom2(chr, coord, highlight, segObj, y, probeAnno, scoreShow = "pt", nrBasesPerSeg, gff, haveLegend=TRUE)
chr |
integer of length 1 with the number of the chromosome for which to make the plot. |
coord |
integer of length 2 with start and end coordinates of the plot. |
highlight |
optional, list with two elements: a single numeric value
coord and a character strand . If present, this
position is marked by a vertical red bar on the coordinate axis. |
segObj |
environment containing three types of data:
1. microarray intensities in along-chromosome order,
2. segmentation (output of findSegments),
3. segment score (dataframe, can
be missing iff nrBasesPerSeg is present),
4. the threshold for "transcribed" segments.
See also Paragraph Intensities in the Details section.
This is currently simply an environment that is expected to contain
certain objects with certain names. In future version, this is
supposed to be replaced by a proper S4 object. |
y |
numeric vector of intensities from a (virtual) array, see Paragraph Intensities in the Details section. |
probeAnno |
environment with probe annotations, see details. |
scoreShow |
character, name of a column in segScore that
is to be used for the coloring of the segments. |
nrBasesPerSeg |
numeric of length 1 with the average number of
nucleotide bases per segment. Can
be missing iff segScore is present. |
gff |
data frame with genome annotation from the GFF file. |
haveLegend |
logical, should the plot contain a legend? |
Intensities: There are two alternative, mutually exclusive ways of providing the intensities to be plotted to this function.
y
and probeAnno
. Then,
y
is a vector of intensities, and probeAnno
is an
environment that contains integer vectors with start positions along
the chromosomes and indices in y
of the probes. For example,
the start positions and indices of probes for the + strand of
chromosome 1 would be described by environment elements
"1.+.start"
and "1.+.index"
, respectively.
segRes
. In that case,
the intended workflow for using this function is as follows:
First, use the script segment.R
to generate a segmentation.
This can be run in parallel on several processors, separately for each
chromosome and strand. The results of this are stored in files of the
name 1.+.rda
, 1.-.rda
, 2.+.rda
, and so forth,
typically within a dedicated directory.
Then, the script viewsegmentation.R
can be used to view the
segmentation results. It collects the R
objects in these
.rda
files into the environment segRes
, with which it calls
this function.
Furthermore, the script scoreSegments.R
can be used to
calculate scores for each segment, which can be passed to this
function using the segRes
argument.
Wolfgang Huber <huber@ebi.ac.uk>
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