add_adapters: Add adapters to probes

In disprose: Discriminating Probes Selection

Add adapters to probes

Description

Add set of adapters to oligonucleotide probes

Usage

add_adapters(
  probe.id.var,
  probe.var,
  ad.len,
  ad.nucl = "t",
  end = c(3, 5),
  mc.cores = 1,
  digits = 4,
  return = "dataframe",
  data,
  data.probe.id.var,
  count.mfe = FALSE,
  RNAfold.path,
  temperature = 40,
  trim.mfe = FALSE,
  MFEmin = 0,
  MFE.files.dir = NULL,
  delete.MFE.files = FALSE,
  verbose = TRUE
)

Arguments

probe.id.var	vector of probes' identification numbers
probe.var	character; character; vector of nucleotide probes
ad.len	integer; vector of adapter length
ad.nucl	character; vector of adapter nucleotides
end	integer; probe's end for adapter attachment. Possible values are 3 and 5.
mc.cores	integer; number of processors for parallel computation (not supported on Windows)
digits	integer; number of decimal places to round the result (MFE)
return	character; returned object; possible values are: "vector" (vector of nucleotide probes with added adapters), "dataframe" (data frame with probes, adapters and their characteristics), "add" (user's data frame with added data of probes, adapters and their characteristics)
data, data.probe.id.var	user's data frame and it's variable with probes identification numbers (used if return = "add")
count.mfe	logical; count minimum folding energy for probes with adapters
RNAfold.path, temperature, trim.mfe, MFEmin, MFE.files.dir, delete.MFE.files	used if count.mfe = TRUE; see count_MFE[disprose] for details
verbose	logical; show messages

Details

ad.len parameter indicates number of ad.nucl repeats. For example, with ad.len =5 for ad.nucl = "t" adapter will be "ttttt" and for ad.nucl = "ac" adapter will be "acacacacac".

ad.len, ad.nucl and end might be vectors of any length. All possible variants of adapters will be added to probes and tested.

For MFE counting ViennaRNA Package (UNIX or Windows) must be installed. see count_MFE[disprose] for details

Value

Vector of nucleotide probes with added adapters, or data frame with probes, adapters and their characteristics, or user's data frame with added data of probes, adapters and their characteristics.

Author(s)

Elena N. Filatova

Examples

probes <- data.frame (ids = 1:3,  probes = c ("acacacacacaca", "aaaaagggggtttttccccc",
                                             "atgcgctagctcagc"))
ad.data <- add_adapters(probe.var = probes$probes, probe.id.var = probes$ids,
                       ad.len = c(5, 8), ad.nucl = c("t", "dt"), end = c(3, 5),
                       count.mfe = FALSE, mc.cores = 1, digits = 4,
                       return = "dataframe", data = probes, data.probe.id.var = probes$ids)

disprose documentation built on March 19, 2022, 2:15 a.m.