[Feature Request] Support ENSEMBL IDs

[lcolladotor]

We should add a is_gencode = TRUE default argument such that when it's set to FALSE, it matches using ENSEMBL IDs instead of Gencode IDs. Aka, it removes the trailing .[0-9] in the IDs.

This should include a unit test that checks the results using the same data with Gencode IDs, then manually makes them ENSEMBL IDs, and checks that with is_gencode = FALSE we get exactly the same results (might have to use set.seed() on this unit test).

[HediaTnani]

This code has been added to the function to support ENSEMBL IDs

`

Check if all rownames start with "ENST"

if (!all(grepl("^ENST", rownames(rse_tx)))) {
stop("Error: Some rownames do not start with 'ENST'.")
}

Check patterns and perform operations based on the patterns

if (all(grepl("^ENST.?\.", rownames(rse_tx)))) {
# If all row names have the format 'ENST00000442987.3'
rse_tx <- rse_tx[rownames(rse_tx) %in% sig_transcripts, , drop = FALSE]
} else if (all(grepl("^ENST", rownames(rse_tx)))) {
# If all row names have the format 'ENST00000442987'
sig_transcripts <- gsub("\..", "", sig_transcripts)
rse_tx <- rse_tx[rownames(rse_tx) %in% sig_transcripts, , drop = FALSE]
} else {
stop("Error: Row names do not match the expected patterns.")
}
`

[HediaTnani]

Unit tests have been implemented here:

qsvaR/tests/testthat/test-getDegTx.R

Lines 60 to 67 in ec138a3

	# Alter the row names of covComb_tx_deg and apply getDegTx
	altered_covComb_tx_deg <- covComb_tx_deg
	rownames(altered_covComb_tx_deg) <- gsub("\\..*", "", rownames(covComb_tx_deg))
	altered_results <- getDegTx(altered_covComb_tx_deg,sig_transcripts =select_transcripts("cell_component"))
	rownames(altered_results) <- rownames(original_results)
	# Test if two objects identical
	expect_identical(original_results, altered_results)
	})