Package 'sccca'

Performs aggregation based on cell clusters and condition. Then, it calculates correlation matrix of genes

Description

This Function is used to perform cell aggregation by averaging the expression of scRNA-seq matrix and then perform correlation matrix

Usage

calculate_cor_mat(expression_mat, condition  = NULL, clusters, assay = "RNA")

Arguments

expression_mat	Seurat object that contains the expression matrix.
condition	column name of the condition in th meta data of the Seurat object.
clusters	column name of the cluster numbers in the meta data of the Seurat object.
assay	the assay to be used default is set to RNA

Value

correlation matrix of genes.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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Calculate cell scores based on number of genes

Description

This Function is used to calculate cell scores based on number of genes

Usage

calculate_normalized_ratio(vec)

Arguments

vec	list of genes of cell types.

Value

vector of cell scores based on the number of overlapped genes with the input matrix.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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Process the cell markers names

Description

This Function is used to return the cell markers names processed for the sctype approach

Usage

correct_gene_symbols(markers)

Arguments

markers

list of unique cell markers.

Value

vector of genes names which overlap with the correlation matrix.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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Performs parallel function on two lists

Description

This Function is used to perform parallel function on two lists

Usage

enrich_genes(ref_list, overlap_list, func)

Arguments

ref_list	reference list.
overlap_list	overlap list.
func	function to be applied.

Value

list where each element is the result of applying the function 'func' to the corresponding elements of 'ref_list' and 'overlap_list'.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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Filter the genes based on specific correlation threshold

Description

This Function is used to filter the gene correlation matrix based on user-defined threshold

Usage

filter_correlation(cor_mat, gene_list, threshold = 0.7)

Arguments

cor_mat	correlation matrix generated from calculate_cor_mat function.
gene_list	cell markers that passed threshold.
threshold	absolute correlation threshold.

Value

vector of gene names that pass user-defined correlation threshold.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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Process the cell markers that overlap between the cell markers and scRNA matrix

Description

This Function is used to return the cell markers that overlap between the cell markers and scRNA matrix

Usage

filter_list(gene_list, passed_cells)

Arguments

gene_list	list of unique genes of cell types.
passed_cells	cells types that pass the specified threshold.

Value

list of cell types which genes are found in the input matrix.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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Performs fisher exact test to get the significant overlap between genes for cell type assignment

Description

This Function is used to perform fisher exact test to get cell types

Usage

fisher_test(ref, gene_overlap)

Arguments

ref	reference gene set.
gene_overlap	genes that pass the correlation threshold.

Value

vector of p-value and overlap.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

Examples

fisher_test(c("PAX8","PAX6","TP53","AOC3","LIPF"), c("LIPF","PAX8","PAX6","TP53","TSHB","AOC3"))

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Process the cell markers that pass specific threshold in the gene correlation matrix

Description

This Function is used to return the cell markers that pass specific threshold in the gene correlation matrix

Usage

match_characters(genes, gene_mat)

Arguments

genes	list of unique genes of cell types.
gene_mat	correlation matrix of genes.

Value

vector of genes names which overlap with the correlation matrix.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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Performs phyper test to get the significant overlap between genes for cell type assignment

Description

This Function is used to perform phyper test to get cell types

Usage

phyper_test(ref, overlap)

Arguments

ref	reference gene set.
overlap	genes that pass the correlation threshold.

Value

vector of p-value and overlap.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

Examples

phyper_test(c("PAX8","PAX6","TP53","AOC3","LIPF"), c("LIPF","PAX8","PAX6","TP53","TSHB","AOC3"))

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Gets the associated cell types using correlation-based approach

Description

This Function is used to get the associated cell clusters using correlation-based approach

Usage

process_clus(cluster,sobj,assay="RNA",clus,markers,cor_m,m_t=0.9,c_t=0.7,test="p")

Arguments

cluster	associated cluster name.
sobj	Seurat object.
assay	assay to be used default is set to RNA.
clus	cell clusters.
markers	cell markers database.
cor_m	gene correlation matrix.
m_t	overlap threshold between cell markers and expression matrix.
c_t	correlation threshold between genes.
test	statistical test that check if overlap is significant could be "p" for phyper or "f" for fisher.

Value

data frame of proposed cell types.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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Process the database for the sctype approach

Description

This Function is used to process the database that will be used for sctype approach

Usage

process_database(database_name = "sctype", org = 'a', tissue, tissue_type = 'n')

Arguments

database_name	name of the database to be used that can be 'sctype' or 'UMD'.
org	name of organism to be used that can be 'h' for human, 'm' for mouse, and 'a' for all markers.
tissue	specified tissue from which the data comes.
tissue_type	tissue type whether 'a' for all types 'n' for normal tissues only or "c" for cancer tissues.

Value

vector of genes names which overlap with the correlation matrix.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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Process the cell markers database and return the processed list

Description

This Function is used to process the cell markers database and return the processed list

Usage

process_markers(markers_df)

Arguments

markers_df

data frame with markers named as gene_original and cell names as cell type.

Value

list of lists of the processed markers

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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Run the pipeline for the cell type assignment

Description

This Function is used to run the main pipeline that does the cell type assignment

Usage

sccca(sobj,assay="RNA",cluster,marker,tissue,tt="a",cond,m_t=0.9,c_t=0.7,test="p",org="a")

Arguments

sobj	Seurat object.
assay	assay to be used default is set to RNA.
cluster	colname in the mata.data that have the cell cluster numbers.
marker	cell markers database path.
tissue	specified tissue from which the data comes.
tt	tissue type whether 'a' for all types 'n' for normal tissues only or "c" for cancer tissues.
cond	colname in the meta.data that have the condition names.
m_t	overlap threshold between cell markers and expression matrix.
c_t	correlation threshold between genes.
test	statistical test that check if overlap is significant could be "p" for phyper or "f" for fisher.
org	organism to be used that can be 'h' for human, 'm' for mouse, and 'a' for all markers.

Value

list of Seurat object that have the assigned clusters, and top 3 proposed cell types.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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Run the sctype approach as it's implemented by Ianevski, A., Giri, A.K. and Aittokallio, T.

Description

This Function is used to run the sctype approach with faster implementation

Usage

sctype(sobj,assay="RNA",tissue,tt="a",clus,org="a",scaled=T,database="sctype")

Arguments

sobj	Seurat object.
assay	assay to be used default is set to RNA.
tissue	specified tissue from which the data comes.
tt	tissue type whether 'a' for all types 'n' for normal tissues only or "c" for cancer tissues.
clus	colname in the mata.data that have the cell cluster numbers.
org	organism to be used that can be 'h' for human, 'm' for mouse, and 'a' for all markers.
scaled	indicates whether the matrix is scaled (TRUE by default)
database	name of the database to be used that can be 'sctype' or 'UMD'

Value

vector of genes names which overlap with the correlation matrix.

Author(s)

Mohmed Soudy [email protected] and Sohpie LE BARS [email protected] and Enrico Glaab [email protected]

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