GlowwormScale: Extract data from Seurat file and scale

In Hannahglover/Glowworm: Mapping genes to single cell RNAseq

Extract data from Seurat file and scale

Usage

GlowwormScale(SeuFile, MetaData, GeneList, PercentCutoff = 0.1)

Arguments

SeuFile	Seurat file
MetaData	A dataframe with barcodes as row names, and either one column of assignments, or two columns of assignments (First column for granular assignments (i.e. Neuro_1), second column for broad assignments (i.e. Neurons))
GeneList	A vector of genes you wish to analyze
PercentCutoff	To remove background signal, clusters which express a candidate gene in less than a percentage of cells will be reduced to zero. Default is 0.1 (10

This function takes a Seurat file, extracts data and merges with metadata. This data is scaled and has background correction

Exports a list containing:

• MetaData - A copy of the metadata

• GlowwormScaleOutput - A scaled data frame of n genes by n populations in metadata

• SumStatsGlobal - A data frame containing Total enrichment score (abundance), SD enrichment score (specificity) and the rank score.
  
  Output list can be used to generate a Scatter plot via GlowwormOutputScatter, a stacked bar plot via GlowwormOutputStacked, or can be used as input for GlowwormSubpopulation

Extract data from Seurat file and scale

Hannahglover/Glowworm documentation built on Jan. 16, 2024, 11:47 p.m.