clusterdend: Clusters for normalized microarray data

Description Usage Arguments Details Value Author(s)

Description

Function to make plots with dendrograms using different clustering methods. Methods are Ward.D2, average and complete with correlations and euclidean distances.

Usage

1
clusterdend(estimates_m = NULL, est_noctrls = NULL, picname, conditions = NULL, colors = NULL, estimates = FALSE, noctrls = TRUE, resDir = NULL)

Arguments

estimates_m

Numeric matrix where columns are samples and rows genes. estimates_m corresponds to the expression matrix with controls.

est_noctrls

Numeric matrix where columns are samples and rows genes. est_noctrls corresponds to the expression matrix without controls.

picname

Character with the output file name.

conditions

Optional. Vector with sample conditions to colour sample names in the plot. conditions vector has to have the same order as the order of samples in the columns of the input expression matrix.

colors

Optional. Vector with colors corresponding to each sample. If this parameter is not defined, default colors will be used.

estimates

If TRUE, clusters for estimates_m are made. Default is FALSE.

noctrls

If TRUE, clusters for est_noctrls are made. Default is TRUE.

resDir

Output results directory. Default is ResultsDir.

Details

This function makes a cluster analysis for a numeric matrix. Optionally two cluster analysis can be made, one for a estimates_m (expression matrix with controls control AffyID) and est_noctrls (expression matrix without controls). Methods used for clustering are: Ward.D2, average and complete with correlations and euclidean distances. Column names in the expression matrix are used as sample names.

Value

This function outputs a .pdf file with several dendrograms for each method and distance.

Author(s)

Magdalena Arnal Segura <marnal@imim.es>


machalen/QualityGraphsOligo documentation built on May 28, 2019, 2:32 a.m.