transform_smat: transform a matrix (center/scaling; truncation; clustering;)...

In nickytong/GenAnalysis: Genomic Analysis

Description

transform a matrix (center/scaling; truncation; clustering;) for heatmap; strongly recommends first apply subsetMainMat to get input mat since some attributes are used

Usage

transform_smat(mat, scale = "row", clusterWithScaledData = FALSE,
  cluster_rows = TRUE, cluster_cols = TRUE,
  clustering_distance_rows = "correlation",
  clustering_distance_cols = "correlation", clustering_method = "ward.D",
  truncate = NA, q1 = 0, q2 = 1, Lower = NULL, Upper = NULL)

Arguments

mat	a matrix, usually from subsetMainMat()
scale	selection from c("none", "row", "column")
clusterWithScaledData	logical indicating if use scaled data for clustering; default is FALSE
cluster_rows	whether to cluster rows
cluster_cols	whether to cluster columns
clustering_distance_rows	distance metric for rows
clustering_distance_cols	distance metric for cols
clustering_method	clustering method
truncate	logical indicating if truncation is needed; default is NA will enable truncate if scale!='none'
q1	parameter q1 to truncByLimit
q2	parameter q2 to truncByLimit
Lower	parameter Lower to truncByQuantile()
Upper	parameter Upper to truncByQuantile()

Value

a matrix with elements gSel, sSel, tree_row, tree_col and so on

nickytong/GenAnalysis documentation built on July 20, 2019, 8:57 a.m.