View source: R/preProcessAdat.R
preProcessAdat | R Documentation |
Pre-process an ADAT file containing raw analyte RFU values in preparation for analysis. For more details please refer to the pre-processing how-to article
preProcessAdat(
adat,
filter.features = TRUE,
filter.controls = TRUE,
filter.qc = TRUE,
filter.outliers = FALSE,
data.qc = NULL,
log.10 = FALSE,
center.scale = FALSE
)
adat |
A |
filter.features |
Logical. Should non-human protein features (SeqIds) be
dropped? Default is |
filter.controls |
Logical. Should SomaScan technical control samples
be dropped? If |
filter.qc |
Logical. If |
filter.outliers |
Logical. Should the |
data.qc |
Character. Character vector of variable names for which data
QC plots are desired. Default is |
log.10 |
Logical. Should the RFU values be log10 transformed?
Default is |
center.scale |
Logical. Should the RFU values be Z-transformed
(centered and scaled)? Default is |
The soma_adat
object is pre-processed with the following steps:
Filter features -> down to human protein analytes
Filter samples -> by the following order and criteria: a) Retain study samples only (dropping buffer, calibrator, and QC samples) b) Only those that pass default normalization acceptance criteria c) Those not identified as outliers.
Data QC -> plots of normalization scale factors by clinical covariates
Transformations -> log10, center, and scale analyte RFU values
A soma_adat
object.
Caleb Scheidel
preProcessAdat(example_data, data.qc = c("Age", "Sex"))
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