Package index • PRECISION.seq.augmented

All functions

biological.effects(): Add biological effects to benchmark data

classification.all(): Apply all classification methods to a precision object

classification.knn(): K-Nearest Neighbors (KNN) Classification

classification.lasso(): Classification with LASSO Logistic Regression

classification.pam(): PAM Classification

classification.ranfor(): Random Forest Classification

classification.svm(): Support Vector Machine (SVM) Classification

cleanup.augmented.data(): Clean Up Cached Augmented Data

cluster.all(): Apply all clustering methods to a precision object

cluster.hc(): Hierarchical clustering for harmonized data

cluster.kmeans(): K-means clustering for harmonized data

cluster.mnm(): Gaussian Mixture Model clustering for harmonized data

cluster.pam(): Partitioning Around Medoids (PAM) clustering for harmonized data

cluster.som(): Self-Organizing Map (SOM) clustering for harmonized data

create.precision.classification(): Create precision object for classification

create.precision.cluster(): Create precision object for clustering

data.benchmark: MiRNA Sequencing Benchmark Data

data.group: Sample Labels of the test and benchmark data

data.miR.info: MiRNA Information

data.test: MiRNA Sequencing Test Data

handling.effects(): Add handling effects to benchmark data

harmon.ComBat.Seq(): Apply ComBat-Seq to Precision Object

harmon.DESeq(): Apply DESeq Harmonization to Precision Object

harmon.PoissonSeq(): Apply PoissonSeq to Precision Object

harmon.QN(): Apply Standard Quantile normalization to Precision Object

harmon.QN.frozen(): Apply Standard Quantile normalization with frozen parameters

harmon.RUVg(): Apply RUVg Harmonization to Precision Object

harmon.RUVr(): Apply RUVr Harmonization to Precision Object

harmon.RUVs(): Apply RUVs Harmonization to Precision Object

harmon.SVA(): Apply SVA Harmonization to Precision Object

harmon.TC(): Apply Total Count (TC) Normalization to Precision Object

harmon.TMM(): Apply TMM Harmonization to Precision Object

harmon.TMM.frozen(): Apply TMM Harmonization with frozen parameters to Precision Object

harmon.UQ(): Perform Upper Quartile (UQ) Normalization

harmon.all(): Apply all harmonization methods to a precision object

harmon.med(): Apply Median Harmonization to Precision Object

load.augmented.data(): Load augmented data from GitHub (with integrity check)

precision-class precision: Precision Class