FilterPlots: FilterPlots

In bicciatolab/PoPsicleR: Pipeline of Preprocessing for Single Cell Experiment

FilterPlots

Description

Apply filters to input data. Creates plot with provided thresholds as input.

Usage

FilterPlots(UMI, G_RNA_low = 0, G_RNA_hi = Inf, U_RNA_low = 0, U_RNA_hi = Inf, percent_mt_hi = 100, percent_ribo_hi = 100, percent_disso_hi = 100, out_folder=getwd())

Arguments

UMI	Input UMI object generated by PrePlots function
G_RNA_low	Minimum number of genes detected in each cell. Default is 0
G_RNA_hi	Maximum number of genes detected in each cell. Default is Infinite
U_RNA_low	Minimum number of molecules detected within a cell. Default is 0
U_RNA_hi	Maximum number of molecules detected within a cell. Default is Infinite
percent_mt_hi	Maximum percentage of mitochondrial genes. Default is 100
percent_ribo_hi	Maximum percentage of ribosomal genes. Default is 100
percent_disso_hi	Maximum percentage of dissociation genes. Default is 100
out_folder	Output folder. Default is working directory

Details

FilterPlots returns two graphs in the "01.QC_Plots" folder:

the first plot (01f) displays data distributions after filtering; filtering thresholds are displayed as gray lines.

the second graph (01g) shows data correlations, that highlight with colors, cells passing the filtering procedure; filtering thresholds are displayed as gray lines.

Value

Returns a Seurat Object filtered according to the user-defined set of thresholds.

Author(s)

Jimmy Caroli, Francesco Grandi

Examples

FilterPlots(umi_object)

FilterPlots(umi_object, G_RNA_low = 500, G_RNA_hi = 10000, U_RNA_low = 1000, U_RNA_hi = 70000, percent_mt_hi = 20, percent_ribo_hi = 50, percent_disso_hi = 10)

bicciatolab/PoPsicleR documentation built on May 7, 2024, 7:26 a.m.