dot-ctss_summary_for_clusters: Summarise CTSSs included in clusters

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Summarise CTSSs included in clusters

Description

Summarise CTSSs included in clusters

Usage

.ctss_summary_for_clusters(ctss, clusters)

Arguments

ctss	A CTSS object.
clusters	A TagClusters, ConsensusClusters or any other object implementing the GRanges class.

Value

The clusters object with a new dominant_CTSS metadata in CTSS format reporting the genomic coordinate and expression score of most highly expressed position in each cluster, plus a nr_ctss metadata reporting the number of expressed CTSSs in each cluster.

Examples

# See also benchmarks/dominant_ctss.md
(ctss <- CTSS( 'chr1', IRanges(start = 1:10, end = 1:10)
             , '+', score = c(1, 0, 0, 1, 2, 0, 2, 1, 0, 1)))
(clusters <- GRanges( 'chr1', IRanges(start = c(1,9)
                    , end = c(8,10)), '+')) |> as("TagClusters")

# The function assumes that all CTSSes have a score above zero
.ctss_summary_for_clusters(ctss[score(ctss)>0], clusters)
# If not the case, it will give incorrect nr_ctss and  fail to remove singletons
.ctss_summary_for_clusters(ctss, clusters)

# The function needs its output to be sorted and is not going to check it.
.ctss_summary_for_clusters(rev(ctss), clusters)
.ctss_summary_for_clusters(ctss, rev(clusters))

# Ties are resolved with 5' preference for both plus and minus strands.
# This may create a small bias.
ctss_minus <- ctss
strand(ctss_minus) <- '-'
clusters_minus <- clusters
strand(clusters_minus) <- '-'
.ctss_summary_for_clusters(ctss_minus, clusters_minus)

charles-plessy/CAGEr documentation built on Oct. 27, 2024, 10:11 p.m.