tss_clustering.Rd
Basic distance and threshold-based clustering of TSSs.
tss_clustering( experiment, samples = "all", threshold = NULL, n_samples = NULL, max_distance = 25, max_width = NULL, singlet_threshold = NULL )
experiment | TSRexploreR object. |
---|---|
samples | A vector of sample names to analyze. |
threshold | TSSs or TSRs with a score below this value will not be considered. |
n_samples | Keep TSS if 'threshold' number of counts is present in n_samples number of samples. |
max_distance | Maximum allowable distance between TSSs for clustering. |
max_width | Maximum allowable TSR width. |
singlet_threshold | TSRs of width 1 must have a score greater than or equal to this threshold to be kept. |
TSRexploreR object with TSRs added to GRanges and data.table counts.
Genes rarely have a single TSS, but rather a cluster of TSSs. This function clusters TSSs into Transcription Start Regions (TSRs). TSSs are clustered if their score is greater than or equal to 'threshold' in at least 'n_samples' number of samples, and are less than or equal to 'max_distance' from each other. The clustered TSSs cannot encompass more than 'max_width' bases. A global singlet threshold can be applied using 'singlet_threshold'.
data(TSSs_reduced) exp <- TSSs_reduced %>% tsr_explorer %>% format_counts(data_type="tss") exp <- tss_clustering(exp, threshold=3)#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored