Annotate Features

Use the ChIPseeker package to annotate TSSs or TSRs relative to known genes or transcripts.

annotate_features(
  experiment,
  data_type = c("tss", "tsr", "tss_diff", "tsr_diff", "shift"),
  feature_type = c("gene", "transcript"),
  genome_annotation = NULL,
  upstream = 1000,
  downstream = 100
)

Arguments

experiment	TSRexploreR object.
data_type	Whether to annotate TSSs ('tss') or TSRs ('tsr').
feature_type	Whether to annotate at the 'gene' or 'transcript' level.
genome_annotation	Genome annotation in GTF, GFF3, or TxDb format.
upstream	Number of bases upstream of TSS for 'promoter' annotation (integer).
downstream	Number of bases downstream of TSS for 'promoter' annotation (integer).

Value

TSRexploreR object with annotation data added to TSS or TSR tables.

Details

This function attempts to assign TSSs or TSRs to the nearest genomic feature. Genomic annotation data can be provided as either a 'GTF' or 'GFF' file, or as a TxDb package from Bioconductor.

'feature_type' allows to you link TSSs or TSRs to genes or transcripts. Furthermore, the size of the promoter region can be defined using 'upstream' and 'downstream', which are relative to the TSSs defined in your annotation data. TSSs or TSRs overlapping a gene on the opposite strand will be marked as 'Antisense'.

Examples

data(TSSs_reduced)
annotation <- system.file("extdata", "S288C_Annotation.gtf", package="TSRexploreR")

exp <- TSSs_reduced %>%
  tsr_explorer(genome_annotation=annotation) %>%
  format_counts(data_type="tss")
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> Warning: The "phase" metadata column contains non-NA values for features of type
#>   stop_codon. This information was ignored.
#> OK

exp <- annotate_features(exp, data_type="tss")
#>