Generate pseudobulk profiles for individuals and calculate correlations (for internal use only)
run_clustering.Rd
Generate pseudobulk profiles for individuals and calculate correlations (for internal use only)
Usage
run_clustering(
per_SNP_sample,
QCed_df,
Sample,
valid_ref_genes,
HE_allele_cell_number_THR = 50,
QC_total_allele_THR = 10,
REMOVE_ESCAPE = TRUE,
PVAL_THR = 0.01,
RHO_THR = 0.5
)
Arguments
- per_SNP_sample
Output from
make_per_SNP_sample_df
function- QCed_df
Output from make_QCed_df
function- Sample
Sample ID
- valid_ref_genes
Output from
Gene_QC
function- HE_allele_cell_number_THR
Threshold for the number of cells expressing reference SNPs. Candidate reference SNPs expressed in at least "HE_allele_cell_number_THR" cells are used for the analysis. Default: 50.
- QC_total_allele_THR
Threshold for the total allele count (depth) of the SNP used for calculating the ratio of expression from Xi. Note that this count is calculated with cells successfully assigned to the group based on the inactivated X chromosome. This filter is applied in the final step of scLinax and differs from "SNP_DETECTION_DP". Default: 10.
- REMOVE_ESCAPE
Boolean:
TRUE (default): Remove ASE profiles of SNPs on escapee genes when calculating correlations between pseudobulk ASE profiles.
FALSE: Include ASE profiles of SNPs on escapee genes when calculating correlations between pseudobulk ASE profiles.
- PVAL_THR
Threshold for P-values and absolute correlation coefficients in the correlation analysis of pseudobulk profiles generated for reference SNPs.
- RHO_THR
Threshold for absolute correlation coefficients in the correlation analysis of pseudobulk profiles generated for reference SNPs.