Description Usage Arguments Value
Read cellranger output directory, filter the data, and return normalized expression matrix
1 2 | get_normalized_expression_matrix(run_to_path_df = data.frame(),
.genome = c("mm10", "hg19"), umi_limits = c(3000, Inf))
|
run_to_path_df: |
A dataframe with two columns (1) run_name (character): The name of the cellranger run, such as patient_id, sample_date, etc... (2) cellranger_path (character): The path to the toplevel cellranger output |
.genome: |
a character, typically 'mm10', or 'hg19'. |
umi_limits: |
vector of length 2, with lower and upper bounds for umi_counts. |
This function reads a series of cellranger output directories. It merges the results together into a large matrix anbd then filters out cells with UMI counts outside of the range specified in umi_limits. Mitochondrial and ribosomal protein-coding genes are then removed from the matrix, as are ENSEMBL IDs with no expression across the remaining cells. Finally, the data is scaled using a global scaling factor (total UMIs per cell) and log2-transformed.
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