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Create a dataframe for QC of candidate reference genes

make_QC_gene_table.Rd

Create a dataframe for QC of candidate reference genes

Usage

make_QC_gene_table(
  QCed_df,
  per_SNP_sample,
  HE_allele_cell_number_THR = 50,
  QC_total_allele_THR = 10
)

Arguments

QCed_df

Output from make_QCed_df function

per_SNP_sample

Output from make_per_SNP_sample_df 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.