QuanRange | R Documentation |

Compute Quantile Range, a metric representing signal strength for QC purpose

Compute Quantile Range, a metric representing signal strength for QC purpose

QuanRange(object, ...) ## S4 method for signature 'NanoStringGeoMxSet' QuanRange(object, split = FALSE, probs, removeoutlier = FALSE, ...) ## S4 method for signature 'matrix' QuanRange(object, probenum, BGmod, probs, removeoutlier = FALSE)

`object` |
count matrix with features in rows and samples in columns |

`...` |
additional argument list that might be used |

`split` |
indicator variable on whether it is for multiple slides |

`probs` |
numeric vector of probabilities with values in [0,1] passed to quantile |

`removeoutlier` |
indicator on whether to remove outliers, default: FALSE |

`probenum` |
a vector of numbers of probes in each gene |

`BGmod` |
a list of sizefact, sizefact, countmat, and id (if it is for multiple slides) |

a valid S4 object with probabilities in phenoData

a matrix of quantile range in rows and probs in columns

data(demoData) demoData <- fitPoisBG(demoData, size_scale = "sum") demoData <- diagPoisBG(demoData) demoData <- aggreprobe(demoData, use = "cor") Biobase::notes(demoData)$disper demoData <- QuanRange(demoData, split = FALSE, probs = c(0.75, 0.8, 0.9, 0.95)) data(demoData) demoData <- fitPoisBG(demoData, groupvar = "slide name") demoData <- diagPoisBG(demoData, split = TRUE) demoData <- aggreprobe(demoData, use = "cor") Biobase::notes(demoData)$disper_sp demoData <- QuanRange(demoData, split = TRUE, probs = c(0.75, 0.8, 0.9, 0.95))

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