factor_sample_filter {scone} | R Documentation

## Factor-based Sample Filtering: Function to filter single-cell RNA-Seq libraries.

### Description

This function returns a sample-filtering report for each cell in the input expression matrix, describing whether it passed filtering by factor-based filtering, using PCA of quality metrics.

### Usage

    factor_sample_filter(
      expr,
      qual,
      gene_filter = NULL,
      max_exp_pcs = 5,
      qual_select_q_thresh = 0.01,
      force_metrics = NULL,
      good_metrics = NULL,
      min_qual_variance = 0.7,
      zcut = 1,
      mixture = TRUE,
      dip_thresh = 0.01,
      plot = FALSE,
      hist_breaks = 20
    )

### Arguments

`expr` | matrix The data matrix (genes in rows, cells in columns).
`qual` | matrix Quality metric data matrix (cells in rows, metrics in columns).
`gene_filter` | Logical vector indexing genes that will be used for PCA. If NULL, all genes are used.
`max_exp_pcs` | numeric number of expression PCs used in quality metric selection. Default 5.
`qual_select_q_thresh` | numeric. q-value threshold for quality/expression correlation significance tests. Default 0.01
`force_metrics` | logical. If not NULL, indexes quality metric to be forcefully included in quality PCA.
`good_metrics` | logical. If not NULL, indexes quality metric that indicate better quality when of higher value.
`min_qual_variance` | numeric. Minimum proportion of selected quality variance addressed in filtering. Default 0.70
`zcut` | A numeric value determining threshold Z-score for sd, mad, and mixture sub-criteria. Default 1.
`mixture` | A logical value determining whether mixture modeling sub-criterion will be applied per primary criterion (quality score). If true, a dip test will be applied to each quality score. If a metric is multimodal, it is fit to a two-component normal mixture model. Samples deviating zcut sd's from optimal mean (in the inferior direction), have failed this sub-criterion.
`dip_thresh` | A numeric value determining dip test p-value threshold. Default 0.05.
`plot` | logical. Should a plot be produced?
`hist_breaks` | hist() breaks argument. Ignored if 'plot=FALSE'.

### Details

None

### Value

A logical, representing samples passing factor-based filter.

### Examples

    mat <- matrix(rpois(1000, lambda = 5), ncol=10)
    colnames(mat) <- paste("X", 1:ncol(mat), sep="")
    qc = as.matrix(cbind(colSums(mat),colSums(mat > 0)))
    rownames(qc) = colnames(mat)
    colnames(qc) = c("NCOUNTS","NGENES")
    mfilt = factor_sample_filter(expr = mat,
        qc, plot = TRUE,qual_select_q_thresh = 1)

[Package scone version 1.18.0 Index]