map_probes: Map 450k/EPIC probes to the reference genome

In pjhop/DNAmCrosshyb: DNAmCrosshyb

Description

Map 450k/EPIC probes to the reference genome

Usage

map_probes(
  probes,
  path,
  array = "450k",
  chromosomes = "all",
  min_width = 15,
  max_width = 50,
  step_size = 5,
  allow_mismatch = FALSE,
  allow_INDEL = FALSE,
  cores = 1,
  verbose = TRUE
)

Arguments

probes	Probe names (450k or EPIC).
path	directory were bisulfite-converted genomes are stored (see details).
array	Array used (450k or EPIC)
chromosomes	Which chromosomes to include (by default: chr1:22, X, Y and M).
min_width	Minimum probe length to map (starting from the 3'-end of the probe).
max_width	Maximum probe length to map (starting from the 3'-end of the probe).
step_size	Map probe lengths from min_width to max_width in these steps.
allow_mismatch	Allow a mismatch in matching? (TRUE/FALSE)
allow_INDEL	Allow an INDEL in matching? (TRUE/FALSE)
cores	Number of cores to use (default = 1).
verbose	Verbose (TRUE/FALSE).

Value

A data frame with one row for each match and .. columns

Probe	Probe ID
chr, start, end, strand	chromosome positions
next_base	base preceding the 'C' base for type I probes
mismatch_pos	position of mismatch (bp from 3'end of probe), NA if exact match
Type2	Type: II, I_Methylated or I_Unmethylated
width	width (in basepairs) of the match
channel	predicted color channel for type I probes

Examples

# Map some probes to all chromosomes, allowing no mismatch/INDELs
probes <- c("cg19883843", "cg24299847", "cg05542153")
## Not run: 
matches <- DNAmCrosshyb::map_probes(probes,
           path = "~/Desktop/genome_bs/hg19",
           chromosomes = "all",
           min_width = 30,
           max_width = 50,
           step_size = 5,
           allow_mismatch = FALSE,
           allow_INDEL = FALSE,
           cores = 1
            )

## End(Not run)

pjhop/DNAmCrosshyb documentation built on June 23, 2021, 1:04 p.m.