README.md

In EDePasquale/Ericas_Functions: A Package of Erica's Most Used Functions for Processing Data Plus Random Utilities

Erica's Functions

A comprehensive set of functions written by or frequently used by Erica DePasquale in her bioinformatics work. Use at your own risk!

Installation

Run the following code to install the package using devtools:

if(!require(devtools)){
  install.packages("devtools") # If not already installed
}
devtools::install_github('EDePasquale/EricasFunctions')

Dependencies

DoubletDecon requires the following R packages:

• Matrix
• Matrix.utils
• data.table
• gdata
• Rtsne
• umap
• dplyr
• DropletUtils

Usage

qc_and_filter()

qc_and_filter(directories, genome = "GRCh38", suffix = "default", min.umis=500, min.genes=250, max.mito=0.3, sig=T, dense=F)

Arguments

• directories - List of directories containing CellRanger output for QC and filtering. Example single directory path is "/Volumes/broad_vangalenlab/depasquale/CellRanger/210628_GeneCounts"
• genome - Desired genome: "GRCh38" and "GRCm38" are accepted, default is "GRCh38"
• suffix - Suffix for directory where the output of this function will be stored and where the input sample sheet is located. Default is the "QC" suffix.
• min.umis - QC filter for minimum number of Unique Molecular Identifiers (UMIs) detected per cell. Default is 500
• min.genes - QC filter for minimum number of genes detected per cell. Default is 250
• max.mito - QC filter to remove cells that exceed this fraction of mitochondrial alignments. Default is 0.3
• sig - Boolean for whether or not to plot cell type signatures. Default is T
• dense - Boolean for whether or not to save dense matrices alongside sparse matrices. Default is F

Value

No return value

cell_signatures()

cell_signatures(coords, expression, signatures, file.path.prefix, cexsize = 1, type = "UMAP", subset = 30:45)

Arguments

• coords - Dataframe containing 2 columns, each for X and Y coordinates with rows as cells
• expression - Dataframe of gene expression values, rows as genes and cells as columns
• signatures - The signatures file, with each column as a seperate list of genes (signature) with headers
• file.path.prefix - File path, including sample name, for plot to be saved as with the appropriate suffix. Example: "/Users/Documents/BPDCN123"
• cexsize - The value that determines "cex" in the plot. Generated as part of the QC and Filter workflow but can be supplied independently. Default is 1
• type - The type of plots to generate/the type of coordinates given. "UMAP" (default) and "tSNE" accepted
• subset - Range of numeric values indicating which 16 plots to generate as the seperate "selected" plots. Default is 30:45 for the Griffin signatures

Value

No return value

random_forest()

random_forest <- function(reference, datasets, results_name="results", ordering_vector="none", cluster_names="none", cluster_colors="none")

Arguments

• reference - Path to a Seurat object that is an integrated reference
• datasets - List of directories containing a Seurat object Example single directory path is "~/Documents/Projects/Data_files_temp/Donor/SBM1014/Seurat.rds"
• results_name - The name you would prefer to call the output directory. Default is "results"
• ordering_vector - A numeric vector containing the order you would like your clusters to appear in the plot, starting with 1. Default is "none", which retains the original order.
• cluster_names - A character vector containing the names of the clusters, in the original order. Default is "none" or cluster numbers to be used.
• cluster_colors - A character vector containing hex codes for the colors of cluster, in the original order. Default is "none" for random colors.

seurat_transfer_data()

seurat_transfer_data <- function(reference, datasets, results_name="results", ordering_vector="none", cluster_names="none", cluster_colors="none")

Arguments

• reference - Path to a Seurat object that is an integrated reference
• datasets - List of directories containing a Seurat object Example single directory path is "~/Documents/Projects/Data_files_temp/Donor/SBM1014/Seurat.rds"
• results_name - The name you would prefer to call the output directory. Default is "results"
• ordering_vector - A numeric vector containing the order you would like your clusters to appear in the plot, starting with 1. Default is "none", which retains the original order.
• cluster_names - A character vector containing the names of the clusters, in the original order. Default is "none" or cluster numbers to be used.
• cluster_colors - A character vector containing hex codes for the colors of cluster, in the original order. Default is "none" for random colors.

scpred()

scpred <- function(reference, datasets, results_name="results", ordering_vector="none", cluster_names="none", cluster_colors="none")

Arguments

• reference - Path to a Seurat object that is an integrated reference
• datasets - List of directories containing a Seurat object Example single directory path is "~/Documents/Projects/Data_files_temp/Donor/SBM1014/Seurat.rds"
• results_name - The name you would prefer to call the output directory. Default is "results"
• ordering_vector - A numeric vector containing the order you would like your clusters to appear in the plot, starting with 1. Default is "none", which retains the original order.
• cluster_names - A character vector containing the names of the clusters, in the original order. Default is "none" or cluster numbers to be used.
• cluster_colors - A character vector containing hex codes for the colors of cluster, in the original order. Default is "none" for random colors.

EDePasquale/Ericas_Functions documentation built on Dec. 17, 2021, 5:38 p.m.