snp_density_primers: Create a density function given a variant output and some...
In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

snp_density_primers

R Documentation

Create a density function given a variant output and some metadata

Description

It is hoped that this will point out regions of a genome which might prove useful when designing PCR primers for a specific condition in a dataset of variants.

Usage

snp_density_primers(
  snp_count,
  pdata_column = "condition",
  condition = NULL,
  cutoff = 20,
  bin_width = 600,
  divide = FALSE,
  topn = 400,
  target_temp = 53,
  max_primer_length = 50,
  bsgenome = "BSGenome.Leishmania.panamensis.MHOMCOL81L13.v52",
  gff = "reference/lpanamensis_col_v46.gff",
  feature_type = "protein_coding_gene",
  feature_start = "start",
  feature_end = "end",
  feature_strand = "strand",
  feature_chr = "seqnames",
  feature_type_column = "type",
  feature_id = "ID",
  feature_name = "description",
  truncate = TRUE,
  xref_genes = TRUE,
  verbose = FALSE,
  min_contig_length = NULL,
  min_gc_prop = 0.25,
  max_nmer_run = 5
)

Arguments

`snp_count`	Result from count_expt_snps()
`pdata_column`	Metadata column containing the condition of interest.
`condition`	Chosen condition to search for variants.
`cutoff`	Minimum number of variants in a region.
`bin_width`	Bin size/region of genome to consider.
`divide`	Normalize by bin width?
`topn`	Keep only this number of candidates.
`target_temp`	Try to get primers with this Tm.
`max_primer_length`	Keep primers at or less than this length.
`bsgenome`	Genome package containing the sequence of interest.
`gff`	GFF to define regions of interest.
`feature_type`	GFF feature type to search against.
`feature_start`	GFF column with the starts (needed?)
`feature_end`	GFF column with the ends (needed?)
`feature_strand`	GFF column with strand information (needed?)
`feature_chr`	GFF column with chromosome information.
`feature_type_column`	GFF column with type information.
`feature_id`	GFF tag with the ID information.
`feature_name`	GFF tag with the names.
`truncate`	Truncate the results to just the columns I think are useful.
`xref_genes`	Cross reference the result against the nearest gene?
`verbose`	Talky talky?
`min_contig_length`	Skip any regions on small contigs?
`min_gc_prop`	Minimum GC content for a suitable primer.
`max_nmer_run`	Filter candidates on maximum nmer runs?