getTxOut: Export sequence of interest from a TxDb object
In TaliaferroLab/rnareachr: Extract Enriched Biological Features From RNA-seq Data

Description Usage Arguments Value See Also Examples

write_Sequence writes gff3 files and/or fasta files from genome TxDb objects subsetted with a transcript list. Sequences extracted can be the entire transcripts (whole) or just the CDS, 3'UTR or 5'UTR sequences. If you instead have sets of genes, we recommend using expression data to find expresed transcripts within your experiment. Alternatively, use gene2tx() to create transcript sets from either make_longest_df or make_median_df

1	write_Sequence(TxDb_gff, tx_list, seq_type, file_name, output_type)

`TxDb_gff`	A TxDb object. Using `filter_Tx` to create this TxDb object is recommended.
`tx_list`	A character list. Must contain Ensembl transcript IDs and be compatible with the gff (the same species).
`seq_type`	One of "whole", "CDS", "5pUTR", or "3pUTR".
`file_name`	A single String. The file type (".fa", ".gff3") will be appended behind the file name.
`output_type`	One of "fa", "gff3", or "both".

write_Sequence creates a named fasta and or gff3 file in the working directory.

filter_Tx, gene2tx, make_longest_df, make_median_df

#generate mydata/hs_test.fa and mydata/hs_test.gff3 containing CDS information for each transcript in hs_tx
hs_filtered_TxDb <- filter_Tx(system.file("extdata", "gencode.v33.annotation.gff3.gz", package = "FeatureReachR"))
hs_tx <- c("ENST00000456328.2", "ENST00000338338.9", "ENST00000356026.10", "ENST00000607222.1", "ENST00000342066.8")
write_Sequence(hs_filtered_TxDb, hs_tx, "CDS", "mydata/hs_test", "both")

#generate mydata/mm_test.fa and mydata/mm_test.gff3 containing 5'UTR information for each transcript in mm_tx
mm_filtered_TxDb <- filter_Tx(system.file("extdata", "gencode.vM20.annotation.gff3.gz", package = "FeatureReachR"))
mm_tx <- c("ENSMUST00000159265.1", "ENSMUST00000027032.5", "ENSMUST00000130201.7", "ENSMUST00000157375.1")
write_Sequence(mm_filtered_TxDb, mm_tx, "UTR5", "mydata/mm_test", "both")