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.