qc.rlsc.wrap {qcrlscR} | R Documentation |
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,
...
)
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'. |
Value
A corrected data frame.
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
res <- qc.rlsc.wrap(data, cls.qc, cls.bl, method, intra, opti, log10,
outl, shift)