Accessors for IsoformicExperiment Objects
Source:R/IsoformicExperiment-methods.R
IsoformicExperiment-accessors.RdS7 generics giving SummarizedExperiment-style access to the three
levels of an IsoformicExperiment. All of them return in-memory tibbles
or matrices; the annotation tables are read from Parquet on first use
and cached (see the class documentation).
Samples
col_data(),col_data<-: sample metadata (sample_idfirst).col_names(): sample IDs of the assays.
Transcript level
assays(),assay(x, name),assay_names(),assay<-: transcript matrices.assay()without a name returns the first assay.row_names(): transcript IDs of the assays.row_data(): transcript annotation (with gene columns) for the assayed transcripts, in assay row order.tx_annot(): the same join for all annotated transcripts.tx_to_gene(): two-column transcript/gene mapping.
Gene level
gene_assays(),gene_assay(x, name),gene_assays<-: gene matrices, derived by summing isoforms unless set explicitly.gene_data(): gene annotation for the genes represented in the assays.gene_names(): gene IDs of the gene assays.
Annotation
annot_data_transcripts(),annot_data_genes(),annot_data_exons(): the raw annotation tables.annot_data(): transcript-centric join of transcripts and genes (exons optional).annot_metadata(): named list describing the annotation source.exon_table(x, gene_name): exons of the transcripts of selected genes.
Housekeeping
clear_cache(): drop cached derived data for the object (and, withannotation = TRUE, the shared annotation tables).
Usage
col_data(self, ...)
col_data(self) <- value
col_names(self, ...)
assays(self, ...)
assay_names(self, ...)
assay(self, name = NULL, ...)
assay(self, name) <- value
row_names(self, ...)
row_data(self, ...)
tx_annot(self, ...)
tx_to_gene(self, ...)
gene_assays(self, ...)
gene_assays(self) <- value
gene_assay(self, name = NULL, ...)
gene_names(self, ...)
gene_data(self, ...)
annot_data_transcripts(self, ...)
annot_data_genes(self, ...)
annot_data_exons(self, ...)
annot_data(self, with_exons = FALSE, ...)
annot_metadata(self, ...)
exon_table(self, gene_name, ...)
clear_cache(self, annotation = FALSE, ...)Arguments
Examples
iso <- example_isoformic()
col_data(iso)
#> # A tibble: 25 × 2
#> sample_id condition
#> <chr> <chr>
#> 1 SRR11498039 preeclampsia
#> 2 SRR11498040 preeclampsia
#> 3 SRR11498041 preeclampsia
#> 4 SRR11498042 preeclampsia
#> 5 SRR11498043 preeclampsia
#> 6 SRR11498044 preeclampsia
#> 7 SRR11498045 preeclampsia
#> 8 SRR11498046 preeclampsia
#> 9 SRR11498063 control
#> 10 SRR11498064 control
#> # ℹ 15 more rows
assay_names(iso)
#> [1] "abundance" "counts"
assay(iso, "abundance")[1:3, 1:3]
#> SRR11498039 SRR11498040 SRR11498041
#> ENST00000374514.8 895.871 850.783 956.829
#> ENST00000420982.5 0.000 0.000 0.000
#> ENST00000374502.7 20.998 16.324 17.151
gene_assay(iso, "abundance")[1:3, 1:3]
#> SRR11498039 SRR11498040 SRR11498041
#> ENSG00000005007.12 3253.512 2563.848 2656.175
#> ENSG00000005206.17 1727.018 1515.008 1807.224
#> ENSG00000007384.15 1970.727 1612.095 2188.516
head(row_data(iso))
#> # A tibble: 6 × 19
#> transcript_id transcript_name transcript_type gene_id gene_name gene_type
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 ENST00000374514.8 LYPLA2-205 protein_coding ENSG00… LYPLA2 protein_…
#> 2 ENST00000420982.5 LYPLA2-206 protein_coding ENSG00… LYPLA2 protein_…
#> 3 ENST00000374502.7 LYPLA2-202 protein_coding ENSG00… LYPLA2 protein_…
#> 4 ENST00000374501.1 LYPLA2-201 protein_coding ENSG00… LYPLA2 protein_…
#> 5 ENST00000436063.7 DNTTIP2-202 protein_coding ENSG00… DNTTIP2 protein_…
#> 6 ENST00000496535.6 DNTTIP2-205 processed_trans… ENSG00… DNTTIP2 protein_…
#> # ℹ 13 more variables: source_gene_id <chr>, source_transcript_id <chr>,
#> # tags <chr>, coding_status <chr>, transcript_support_level <chr>,
#> # tie_score <dbl>, cds_start <int>, cds_end <int>, cds_length <int>,
#> # is_canonical <lgl>, haplotype <chr>, n_exons <int>, tx_length <int>
head(gene_data(iso))
#> # A tibble: 6 × 14
#> gene_id gene_name gene_type source_gene_id gene_class gene_category dhs_type
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 ENSG0000… UPF1 protein_… NA NA NA NA
#> 2 ENSG0000… SPPL2B protein_… NA NA NA NA
#> 3 ENSG0000… RHBDF1 protein_… NA NA NA NA
#> 4 ENSG0000… PIGQ protein_… NA NA NA NA
#> 5 ENSG0000… MED24 protein_… NA NA NA NA
#> 6 ENSG0000… REV3L protein_… NA NA NA NA
#> # ℹ 7 more variables: coding_status <chr>, cumulative_support <chr>,
#> # haplotype <chr>, seqid <chr>, start_pos <int>, end_pos <int>, strand <chr>
head(exon_table(iso, "RBPJ"))
#> # A tibble: 6 × 12
#> gene_id gene_name transcript_id transcript_name transcript_type haplotype
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> 2 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> 3 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> 4 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> 5 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> 6 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> # ℹ 6 more variables: exon_id <chr>, exon_number <int>, seqid <chr>,
#> # start_pos <int>, end_pos <int>, strand <chr>