Usage
get.mgi.features( file = "http://cgd.jax.org/tools/SNPtools/MGI/MGI.20130305.sorted.txt.gz", chr = NULL, start = NULL, end = NULL, source = c("all", "MGI", "VEGA", "ENSEMBL", "Blat", "NCBI_Gene"), type = c("all", "gene", "pseudogenic_transcript", "pseudogenic_exon", "pseudogene", "match", "match-part", "transcript", "exon", "mRNA", "five_prime_UTR", "start_codon", "CDS", "stop_codon", "three_prime_UTR", "pseudogenic_mRNA", "pseudogenic_start_codon", "pseudogenic_CDS", "pseudogenic_stop_codon", "pseudogenic_five_prime_UTR", "pseudogenic_three_prime_UTR", "sequence_feature"))
Arguments
file
character, the full path to the Tabix indexed and zipped MGI feature file. Default = "http://cgd.jax.org/tools/SNPtools/MGI/MGI.20130305.sorted.txt.gz" for internal JAX use.
chr
Numeric vector, chr for each start and end position. Chr, start and end must all have the same length.
start
Numeric vector, start position in Mb or bp for each chr. Chr, start and end must all have the same length.
end
Numeric vector, end position in Mb or bp for each chr. Must be greater than or equal to the corresponding start value. Chr, start and end must all have the same length.
source
Character vector, the source of the annotation. Options are ("all", "MGI", "VEGA", "ENSEMBL", "Blat", "NCBI_Gene"). "all" returns all features.
type
Character vector, the type of feature. Options are ("all", "gene", "pseudogenic_transcript", "pseudogenic_exon", "pseudogene", "match", "match-part", "transcript", "exon", "mRNA", "five_prime_UTR", "start_codon", "CDS", "stop_codon", "three_prime_UTR", "pseudogenic_mRNA", "pseudogenic_start_codon", "pseudogenic_CDS", "pseudogenic_stop_codon", "pseudogenic_five_prime_UTR", "pseudogenic_three_prime_UTR", "sequence_feature"). "all" returns all features.