map_probes_sequence: Map 450k/EPIC probes to a user-defined sequence

In pjhop/DNAmCrosshyb: DNAmCrosshyb

Description

Map 450k/EPIC probes to a user-defined sequence

Usage

map_probes_sequence(
  sequence,
  next_base,
  prev_base,
  array = c("450k", "EPIC"),
  max_width = 50,
  min_width = 15,
  step_size = 5,
  allow_mismatch = FALSE,
  max_mismatch = 1,
  allow_indel = FALSE,
  min_distance = 6,
  use_Y = TRUE,
  methylation_status = "methylated",
  verbose = TRUE,
  cores = 1
)

Arguments

sequence	DNA sequence (string)
next_base	Base following the end of the sequence (necessary to know for bisulfite conversion)
prev_base	Base preceding the start of the sequence (necessary to know for bisulfite conversion)
array	Array used (450k or EPIC)
max_width	Maximum probe length to map (starting from the 3'-end of the probe).
min_width	Minimum 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)
max_mismatch	Maximum number of allowed mismatches
allow_indel	Allow an INDEL in matching? (TRUE/FALSE)
min_distance	Minimum distance from 3'end of probe where mismatches/indels are allowed
use_Y	Use Y (IUPAC) to represent Cs in CpG-sites?
methylation_status	Assumed CpG-sites are either methylated or unmethylated (argument not used if use_Y == TRUE)
verbose	Should function be verbose? (TRUE/FALSE)
cores	Number of cores to use (default = 1).

Value

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

Probe	Probe ID
start, end, strand	positions
width	width (in basepairs) of the match
sbe_site	base preceding the match
mismatch_pos	position of mismatch (bp from 3'end of probe), NA if exact match
indel_pos	position of INDEL (bp from 3'end of probe), NA if exact match
width_incl_indel	width of match including INDEL, NA if exact match
sequence_bs	bisulfite-converted sequence
Type2	Type: II, I_Methylated or I_Unmethylated
channel	predicted color channel for type I probes

Examples

# Map probes to the C9orf72 hexanucleotide repeat
repeat_sequence <- paste(rep("GGCCCC", 10), collapse="")
matches_c9 <- map_probes_sequence(sequence = repeat_sequence, next_base = "G", prev_base = "C",
                                  array = "450k", min_width = 10, max_width = 25, allow_indel = FALSE, 
                                  allow_mismatch = TRUE, min_distance = 6,
                                  step_size = 1, use_Y = FALSE, methylation_status = "methylated")
head(matches_c9 %>% data.frame())

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