Filter dataset according to QC parameter criteria, remove features that are internal standards (ISTDs) or not annotated as quantifier (optional). Exclude features and analyses that were annotated as not valid in the metadata (VALID_INTEGRATION, VALID_ANALYSIS).
Note: When exclude_istds is FALSE, then SB_RATIO_min is ignored, because the the S/B is based on Processed Blanks (PBLK) that contain ISTDs.
Usage
apply_qc_filter(
data,
Intensity_BQC_min = NA,
CV_BQC_max = NA,
Intensity_TQC_min = NA,
CV_TQC_max = NA,
SB_RATIO_min = NA,
R2_min = NA,
RQC_CURVE = NA,
quantifier_only = TRUE,
exclude_istds = TRUE,
features_to_keep = NULL
)Arguments
- data
MidarExperiment object
- Intensity_BQC_min
Minimum median signal intensity of BQC
- CV_BQC_max
= Maximum %CV of BQC
- Intensity_TQC_min
Minimum median signal intensity of TQC
- CV_TQC_max
Maximum %CV of TQC
- SB_RATIO_min
= Signal-to-Blank ratio. Calculated from the 10% percentile of all samples and the median of the Process Blank (PBLK)
- R2_min
= Minimum r squared of RQC curve defined under
RQC_CURVE- RQC_CURVE
Name of RQC curve as string, or index number of curve to use for filtering (first curve is 1)
- quantifier_only
Remove features where Quantifier is set to FALSE.
- exclude_istds
Remove Internal Standards (ISTD). If set to FALSE, meaning ISTDs will be included, then
SB_RATIO_minis ignored, because the the S/B is based on Processed Blanks (PBLK) that contain ISTDs.- features_to_keep
Features that must be kept, even if they did not meet the given QC criteria