Decompose tag cluster into subclusters according to CTSS expression fraction of local maxima CTSS expression. Performs local summit decomposition for each local maxima separately in decreasing order of expression level. For each local summit decomposition, subclusters will be merged if within maxGap distance. If smoothPad>0, neighbouring non-zero CTSSs within smoothPad distance of CTSSs fulfilling the summit fraction criterion will also be included. Final subclusters within mergeDist bp will be merged.
Source:R/decompose.R
local_maxima_decompose.RdDecompose tag cluster into subclusters according to CTSS expression fraction of local maxima CTSS expression. Performs local summit decomposition for each local maxima separately in decreasing order of expression level. For each local summit decomposition, subclusters will be merged if within maxGap distance. If smoothPad>0, neighbouring non-zero CTSSs within smoothPad distance of CTSSs fulfilling the summit fraction criterion will also be included. Final subclusters within mergeDist bp will be merged.
Usage
local_maxima_decompose(
views,
fraction = 0.1,
maximaDist = 20,
maxGap = maximaDist,
mergeDist = -1,
smoothPad = 0
)Arguments
- views
A
Viewsobject of tag clusters.- fraction
The fraction of the summit CTSS expression that a CTSS must have to be considered part of the tag cluster.
- maximaDist
The distance within which local maxima are considered.
- maxGap
The distance within which subclusters will be merged.
- mergeDist
The distance within which final decomposed subclusters will be merged.
- smoothPad
The distance within which neighbouring non-zero CTSSs will be included.