This function takes either a gene name or sequence coordinates and returns an ape object with DNA sequence from the the selected genome reference. You can choose from hg38 and GRCz11. Features are generated from ensembl GFF files. Features overlapping the query range (gene or sequence) are returned as a GRanges object and as features within the Ape object. The features included can optionally be filtered using the "include_type" argument to the function. Using the "additional_granges" argument, you can provide additional features not present in the standard gene model which will be added to the Ape object GRanges slot and to the features slot.
Usage
bb_make_ape_genomic(
query,
genome = c("hg38", "GRCz11"),
extend_left = 0,
extend_right = 0,
include_type = c("ncRNA_gene", "rRNA", "exon", "pseudogene", "pseudogenic_transcript",
"ncRNA", "gene", "CDS", "lnc_RNA", "mRNA", "three_prime_UTR", "five_prime_UTR",
"unconfirmed_transcript", "scRNA", "C_gene_segment", "D_gene_segment",
"J_gene_segment", "V_gene_segment", "miRNA", "tRNA", "snRNA", "snoRNA",
"lincRNA_gene", "lncRNA_gene", "unconfirmed_transcript"),
additional_granges = NULL
)Arguments
- query
Either a valid gene name or a named numeric vector of genome coordinates. This vector should be of the form: c(chr = 1, start = 1000, end = 2000). The vector must be numeric an must have those names. The chromosome number will be converted to "chr1" etc internally.
- genome
The genome to pull from, Default: c("hg38", "GRCz11")
- extend_left
Number of bases to extend the query to the left or "upstream" relative to the + strand.
- extend_right
Number of bases to extend the query to the right or "downstream" relative to the + strand.
- include_type
The type of features to include from the standard gene model. Default: c("ncRNA_gene", "rRNA", "exon", "pseudogene", "pseudogenic_transcript", "ncRNA", "gene", "CDS", "lnc_RNA", "mRNA", "three_prime_UTR", "five_prime_UTR", "unconfirmed_transcript", "scRNA", "C_gene_segment", "D_gene_segment", "J_gene_segment", "V_gene_segment", "miRNA", "tRNA", "snRNA", "snoRNA", "lincRNA_gene", "lncRNA_gene", "unconfirmed_transcript")
- additional_granges
A GRanges object with features to add to the Ape Object. Coordinates should all be relative to the reference, NOT the sequence extracted for the ape file. The Granges object can be constructed with the following syntax: GenomicRanges::makeGRangesFromDataFrame(data.frame(seqname = "chr6", start = 40523370, end = 40523380, strand = "+", type = "addl_feature", gene_name = "prkcda", label = "feature1"), keep.extra.columns = T). The gene_name argument here is optional. If you have defined features based on the extracted sequence, (i.e. relative to position 1 in the ORIGIN section of the Ape object), the best option is to use the feature setting function FEATURES(instance_of_Ape) <- GRanges_Object.