Call ATAC-seq sample outliers

Identify samples that are outside of 3 times the interquartile range of principal components that explain at least 7.5% of variance in each tissue. Use only the 10,000 most variable peaks. Outlier calling is performed separately in each sex. This specifies ATAC-seq outliers excluded from differential analysis by MoTrPAC.

Usage

atac_call_outliers(tissues, scratchdir = ".")

Arguments

tissues

character vector of tissue abbreviations for which to call ATAC-seq outliers, one of "BAT", "HEART", "HIPPOC", "KIDNEY", "LIVER", "LUNG", "SKM-GN", "WAT-SC"

scratchdir

character, local directory in which to download data from Google Cloud Storage. Current working directory by default.

Value

NULL if there are no outliers, or a data frame with three columns and one row per outlier:

viallabel

character, sample identifier

tissue

character, tissue abbreviation, one of MotrpacRatTraining6moData::TISSUE_ABBREV

reason

character, PC(s) in which the sample was flagged

See also

call_pca_outliers() for workhorse function and plot_pcs() for plotting function

Examples

if (FALSE) { # \dontrun{
atac_call_outliers("LIVER","/tmp")
atac_call_outliers(c("LIVER","BAT"),"/tmp")
} # }