add_adapters {disprose} | R Documentation |
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: |
data , data.probe.id.var |
user's data frame and it's variable with probes identification numbers (used if |
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 |
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)