get_reduced_dimensions_MDS_bulk: Get dimensionality information to a tibble using MDS

In tidybulk: Brings transcriptomics to the tidyverse

Description

Get dimensionality information to a tibble using MDS

Usage

get_reduced_dimensions_MDS_bulk(
  .data,
  .element = NULL,
  .feature = NULL,
  .abundance = NULL,
  .dims = 2,
  top = 500,
  of_samples = TRUE,
  log_transform = TRUE
)

Arguments

.data	A tibble
.element	A column symbol. The column that is used to calculate distance (i.e., normally samples)
.feature	A column symbol. The column that is represents entities to cluster (i.e., normally genes)
.abundance	A column symbol with the value the clustering is based on (e.g., 'count')
.dims	A integer vector corresponding to principal components of interest (e.g., 1:6)
top	An integer. How many top genes to select
of_samples	A boolean
log_transform	A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data)

Value

A tibble with additional columns

tidybulk documentation built on April 7, 2021, 6 p.m.