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Summarize scLinaX-multi results

summarize_scLinaX_multi.Rd

Summarize scLinaX-multi results

Usage

summarize_scLinaX_multi(phased_df, QC_total_allele_THR = 10, Annotation = NULL)

Arguments

phased_df

A dataframe generated by the run_scLinaX_multi function.

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.

Annotation

A dataframe (tibble) for the annotation of the cells. This dataframe should have the following columns:

  • cell_barcode

  • Annotation

Value

A dataframe (tibble) containing scLinaX-multi results.

If no Annotation is supplied, this function returns the ratio of accessible chromatin derived from the inactivated X chromosome for all cells. If Annotation is supplied, this function returns the ratio of accessible chromatin derived from the inactivated X chromosome for each cell annotation.

The dataframe includes the following columns:

  • Sample_ID: Sample ID

  • SNP_ID: SNP identifier

  • CHR: PAR or nonPAR

  • POS: Genomic position of the SNP (GRCh38)

  • REF: Reference allele of the SNP A,T,G,C

  • ALT: Alternative allele of the SNP A,T,G,C

  • REFcount: Allelic read count of the reference allele

  • ALTcount: Allelic read count of the alternative allele

  • OTHcount: Allelic read count of the other allele

  • Peak_name: Name of the peak

  • Gene: Nearest gene to the peak

  • XCI_status: XCI status escape, variable, inactive, unknown

  • Gene_class: XCI status combined with CHR information PAR1, nonPAR_escape, nonPAR_variable, nonPAR_inactive, nonPAR_unknown, PAR2

  • A_allele_count, B_allele_count: Total allele count of allele A and B

  • Total_allele_count: Total allele count

  • minor_allele_ratio: Ratio of the accessible chromatin derived from the allele (A, B) with lower expression (=Ratio of the accessible chromatin derived from Xi)

  • Major_allele: The allele with the higher read count A, B

If in per-cell annotation mode, it includes the additional column:

  • Annotation: Cell annotation