calc_agg_bulk: Calculate UPM expression values across pData values

In kgellatl/SignallingSingleCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

Description

This will calculate UMIs per million UPM expression values across pData columns. Useful for heatmaps and networking analysis.

Usage

calc_agg_bulk(
  input,
  aggregate_by,
  group_by = FALSE,
  cutoff_frac = FALSE,
  cutoff_num = FALSE,
  cutoff_cpm = FALSE
)

Arguments

input	the input ex_sc.
aggregate_by	The pData variables to break by
group_by	The pData variables that contains distinct groups if included in aggregate_by (eg Timepoint, Condition, etc) This is used to calculate portions internally to this group
cutoff_frac	a fraction expressing value below which gene expression values will be set to 0 for the mean.
cutoff_num	a total number cells expressing value below which gene expression values will be set to 0 for the mean.
cutoff_cpm,	the minimum CPM values below which set to 0 This is useful for removing nodes from networks that contain only a couple of cells.

Details

Utilize information stored in pData to control the plot display.

Examples

plot_tsne_metadata(ex_sc_example, color_by = "UMI_sum", title = "UMI_sum across clusters", facet_by = "Cluster", ncol = 3)

kgellatl/SignallingSingleCell documentation built on Dec. 29, 2021, 4:12 p.m.