qcrlscR (version 0.1.3)

qc.rlsc.wrap: Wrapper function for QC-RLSC

Description

Wrapper function for QC-RLSC

Usage

qc.rlsc.wrap(
  dat,
  cls.qc,
  cls.bl,
  method = c("subtract", "divide"),
  intra = FALSE,
  opti = TRUE,
  log10 = TRUE,
  outl = TRUE,
  shift = TRUE,
  ...
)

Value

A corrected data frame.

Arguments

dat

A data frame with samples (row) and variables (column).

cls.qc

A vector with string of "qc" and "sample".

cls.bl

A vector with string of batch indicators.

method

Data scaling method. Support "subtract" and "divide"

intra

A logical value indicating whether signal correction is performed inside each batch ("intra-batch") or not ("inter-batch").

opti

A logical value indicating whether or not 'span' parameters are optimised.

log10

A logical value indicating whether log10 transformation for the data set or not. If the transformation is applied, the reverse procedure will be performed.

outl

A logical value indicating whether or not QC outlier detection is employed. If TRUE, the QC outlier will be assigned as the median of QC.

shift

A logical value indicating whether or not batch shift is applied after signal correction.

...

Other parameter for 'loess'.

See Also

Other QC-RLSC function: qc.rlsc()

Examples

names(man_qc)
data <- man_qc$data
meta <- man_qc$meta

cls.qc <- factor(meta$sample_type)
cls.bl <- factor(meta$batch)

## apply  QC-RLSC wrapper function
method <- "divide"     # "subtract"
intra <- TRUE
opti <- TRUE
log10 <- TRUE
outl <- TRUE
shift <- TRUE

# \donttest{
res <- qc.rlsc.wrap(data, cls.qc, cls.bl, method, intra, opti, log10,
                    outl, shift)
# }