exportToBed {CAGEr} | R Documentation |
Creates BED file(s) with track(s) of individual CTSSs, tag clusters or consensus clusters. CTSSs and consensus clusters can be optionally colored in the color of their expression class. Tag clusters and consensus clusters can be displayed in a gene-like representation with a line showing full span on the cluster, filled block showing interquantile range and a thick box denoting position of the dominant (most frequently used) TSS.
exportToBed(object, what = c("CTSS", "tagClusters", "consensusClusters"), qLow = NULL, qUp = NULL, colorByExpressionProfile = FALSE, oneFile = TRUE) ## S4 method for signature 'CAGEr' exportToBed(object, what = c("CTSS", "tagClusters", "consensusClusters"), qLow = NULL, qUp = NULL, colorByExpressionProfile = FALSE, oneFile = TRUE)
object |
A |
what |
Which elements should be exported to BED track. Can be |
qLow, qUp |
Position of which "lower" (resp. "upper") quantile should be used as 5'
(resp. 3') boundary of the filled block in gene-like representation of the cluster.
Default value |
colorByExpressionProfile |
Logical, should blocks be colored in the color of their
corresponding expression class. Ignored when |
oneFile |
Logical, should all CAGE datasets be exported as individual tracks into the
same BED file (TRUE) or into separate BED files (FALSE). Ignored when |
This function creates various representations of CTSSs, tag clusters and consensus clusters in the BED format, which can be directly visualised in the UCSC Genome Browser.
When what = "CTSS"
, one BED file with single track of 1 bp blocks representing all
detected CTSSs (in all CAGE samples) is created. CTSSs can be colored according to their
expression class (provided the expression profiling of CTSSs was done by calling
getExpressionProfiles
function). Colors of expression classes match the colors
in which they are shown in the plot returned by the plotExpressionProfiles
function. For colorByExpressionProfile = FALSE
, CTSSs included in the clusters are
shown in black and CTSSs that were filtered out in gray.
When what = "tagClusters"
, one track per CAGE dataset is created, which can be
exported to a single BED file (by setting oneFile = TRUE
) or separate BED files
(by setting oneFile = FALSE
). In case qLow = NULL
and qUp = NULL
,
TCs are represented as simple blocks showing only the full span of TC from the start to
the end. Setting qLow
and/or qUp
parameters to a value of the desired quantile
creates a gene-like representation with a line showing full span of the TC, filled block
showing specified interquantile range and a thick 1bp block denoting position of the dominant
(most frequently used) TSS. All TCs in one track (one CAGE dataset) are shown in the same
color.
When what = "consensusClusters"
consensus clusters are exported to BED file. Since
there is only one set of consensus clusters common to all CAGE datasets, only one track is
created in case of a simple representation. This means that when qLow = NULL
and
qUp = NULL
one track with blocks showing the full span of consensus cluster from
the start to the end is created. However, the distribution of the CAGE signal within
consensus cluster can be different in different CAGE samples, resulting in different
positions of quantiles and dominant TSS. Thus, when qLow
and/or qUp
parameters
are set to a value of the desired quantile, a separate track with a gene-like representation
is created for every CAGE dataset. These tracks can be exported to a single BED file (by
setting oneFile = TRUE
) or separate BED files (by setting oneFile = FALSE
).
The gene-like representation is analogous to the one described above for the TCs. In all
cases consensus clusters can be colored according to their expression class (provided the
expression profiling of consensus clusters was done by calling
getExpressionProfiles
function). Colors of expression classes match the colors
in which they are shown in the plot returned by the plotExpressionProfiles
function. For colorByExpressionProfile = FALSE
all consensus clusters are shown in
black.
Creates BED file(s) in the working directory that can be directly visualised as custom tracks in the UCSC Genome Browser.
Vanja Haberle
Other CAGEr export functions: exportCTSStoBedGraph
### exporting CTSSs colored by expression class exportToBed(object = exampleCAGEset, what = "CTSS", colorByExpressionProfile = TRUE) ### exporting tag clusters in gene-like representation exportToBed( object = exampleCAGEset, what = "tagClusters" , qLow = 0.1, qUp = 0.9, oneFile = TRUE) exportToBed( object = exampleCAGEexp, what = "tagClusters" , qLow = 0.1, qUp = 0.9, oneFile = TRUE)