Convert transcripts to genes

Convert transcripts to genes

Usage

convertTranscriptsToGenes(object, ...)

# S4 method for Matrix
convertTranscriptsToGenes(object, tx2gene, aggregate = TRUE)

# S4 method for SummarizedExperiment
convertTranscriptsToGenes(object)

# S4 method for character
convertTranscriptsToGenes(object, tx2gene)

# S4 method for matrix
convertTranscriptsToGenes(object, tx2gene, aggregate = TRUE)

Arguments

object

Object.

tx2gene

TxToGene. Transcript-to-gene mappings.

aggregate

logical(1). For objects supporting dim(), aggregate counts to gene level and collapse the matrix.

...

Additional arguments.

Value

• character: factor. Genes in the values, transcripts in the names.

• matrix, Matrix, SummarizedExperiment: Object containing counts collapsed to gene level by default (see aggregate argument).

Note

For objects containing a count matrix, the object rows will be collapsed to gene level using aggregate(). This applies to our SummarizedExperiment method.

Updated 2021-09-13.

See also

• aggregate().

Examples

data(SummarizedExperiment_transcripts, package = "AcidTest")
txse <- SummarizedExperiment_transcripts
object <- txse

t2g <- TxToGene(object)
print(t2g)
#> TxToGene with 6 rows and 2 columns
#>                                txId             geneId
#>                         <character>        <character>
#> ENST00000371584.8 ENST00000371584.8 ENSG00000000419.12
#> ENST00000371588.9 ENST00000371588.9 ENSG00000000419.12
#> ENST00000413082.1 ENST00000413082.1 ENSG00000000419.12
#> ENST00000494424.1 ENST00000494424.1 ENSG00000000003.15
#> ENST00000496771.5 ENST00000496771.5 ENSG00000000003.15
#> ENST00000612152.4 ENST00000612152.4 ENSG00000000003.15
transcripts <- rownames(object)
print(transcripts)
#> [1] "ENST00000494424.1" "ENST00000496771.5" "ENST00000612152.4"
#> [4] "ENST00000371584.8" "ENST00000371588.9" "ENST00000413082.1"

## character ====
## Returns as factor.
x <- convertTranscriptsToGenes(transcripts, tx2gene = t2g)
print(x)
#>  ENST00000494424.1  ENST00000496771.5  ENST00000612152.4  ENST00000371584.8 
#> ENSG00000000003.15 ENSG00000000003.15 ENSG00000000003.15 ENSG00000000419.12 
#>  ENST00000371588.9  ENST00000413082.1 
#> ENSG00000000419.12 ENSG00000000419.12 
#> Levels: ENSG00000000003.15 ENSG00000000419.12
str(x)
#>  Factor w/ 2 levels "ENSG00000000003.15",..: 1 1 1 2 2 2
#>  - attr(*, "names")= chr [1:6] "ENST00000494424.1" "ENST00000496771.5" "ENST00000612152.4" "ENST00000371584.8" ...

## matrix ====
## Note that transcript IDs currently must be in the rows.
counts <- counts(object)
print(counts)
#>                   sample1 sample2 sample3 sample4
#> ENST00000494424.1       1       2       3       4
#> ENST00000496771.5       5       6       7       8
#> ENST00000612152.4       9      10      11      12
#> ENST00000371584.8      13      14      15      16
#> ENST00000371588.9      17      18      19      20
#> ENST00000413082.1      21      22      23      24
## Aggregate to gene level.
x <- convertTranscriptsToGenes(counts, tx2gene = t2g, aggregate = TRUE)
print(x)
#>                    sample1 sample2 sample3 sample4
#> ENSG00000000003.15      15      18      21      24
#> ENSG00000000419.12      51      54      57      60
colSums(x)
#> sample1 sample2 sample3 sample4 
#>      66      72      78      84 
## Simply map to rownames.
x <- convertTranscriptsToGenes(counts, tx2gene = t2g, aggregate = FALSE)
print(x)
#>                    sample1 sample2 sample3 sample4
#> ENSG00000000003.15       1       2       3       4
#> ENSG00000000003.15       5       6       7       8
#> ENSG00000000003.15       9      10      11      12
#> ENSG00000000419.12      13      14      15      16
#> ENSG00000000419.12      17      18      19      20
#> ENSG00000000419.12      21      22      23      24
colSums(x)
#> sample1 sample2 sample3 sample4 
#>      66      72      78      84 

## SummarizedExperiment ====
x <- convertTranscriptsToGenes(object)
print(x)
#> class: SummarizedExperiment 
#> dim: 2 4 
#> metadata(0):
#> assays(1): counts
#> rownames(2): ENSG00000000003.15 ENSG00000000419.12
#> rowData names(0):
#> colnames(4): sample1 sample2 sample3 sample4
#> colData names(0):