In the output file
output.bus, equivalence classes (EC) are denoted by
an index, which is related to the set of transcripts the EC is compatible to
in the output file
matrix.ec. This function further relates the set of
transcripts to the set of genes the EC is compatible to. This function first
matrix.ec, and then translates the transcripts into genes.
EC2gene(tr2g, kallisto_out_path, verbose = TRUE)
A Data frame with columns
Path to the
Logical, whether to display progress.
The data frame passed to
tr2g can be generated from function
transcript2gene in this package for any organism that has gene and
transcript ID on Ensembl, or from the
tr2g_* family of function.
You no longer need to use this function before running
the purpose of this function is to query which genes equivalence classes map
Calling this function is unnessary when working with gene count matrices. However, this function is useful for finding genes the ECs map to in TCC matrices, such as when finding species-specific ECs in mixed species datasets and identifying ECs mapped to known marker genes of cell types.
A data frame with 3 columns:
Index of the EC as appearing in the
A list column each element of which is a numeric vector of the transcripts in the EC corresponding to the EC index. To learn more about list columns, see the relevant section in the R for Data Science book.
A list column each element of which is a character vector of genes the EC maps to.
# Load toy example for testing
toy_path <- system.file("testdata", package = "BUSpaRse")
load(paste(toy_path, "toy_example.RData", sep = "/"))
EC2gene(tr2g_toy, toy_path, verbose = FALSE)
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