vec_to_genomic_ranges: Convert sequence strings to GenomicRanges object

In TmCalculator: Genome-Wide Nucleic Acid Melting Temperature Profiling and Multi-Omics Integration

Convert sequence strings to GenomicRanges object

Description

This function converts sequence strings to a GenomicRanges object, handling both named and unnamed sequences. It can also process complementary sequences if provided. sequence names can be in the format ">chr2:1-10:+:seq2" which will be parsed into chromosome, position, strand, and name components.

Usage

vec_to_genomic_ranges(input_seq)

Arguments

input_seq

A character vector of sequences. If named with format "chr2:1-10:[+|-]:[seq_name]" the name will be parsed into GRanges components.

Value

A GenomicRanges object containing: - GRanges information (seqnames, ranges, strand) - sequence data - Complementary sequences - Names from input or auto-generated

Examples

# Example with named sequences in GRanges format
seqs <- c("ATGCG", "GCTAG")
names(seqs) <- c("chr1:1111-1115:+:seq1", "chr2:1221-1225:+")
gr <- vec_to_genomic_ranges(seqs)

# Example with unnamed sequences
seqs <- c("ATGCG", "GCTAG")
gr <- vec_to_genomic_ranges(seqs)

TmCalculator documentation built on Aug. 28, 2026, 5:09 p.m.