% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sample_filtering.R
\title{Factor-based Sample Filtering: Function to filter single-cell RNA-Seq 
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)
\item{expr}{matrix The data matrix (genes in rows, cells in columns).}

\item{qual}{matrix Quality metric data matrix (cells in rows, metrics in 

\item{gene_filter}{Logical vector indexing genes that will be used for PCA. 
If NULL, all genes are used.}

\item{max_exp_pcs}{numeric number of expression PCs used in quality metric 
selection. Default 5.}

\item{qual_select_q_thresh}{numeric. q-value threshold for 
quality/expression correlation significance tests. Default 0.01}

\item{force_metrics}{logical. If not NULL, indexes quality metric to be 
forcefully included in quality PCA.}

\item{good_metrics}{logical. If not NULL, indexes quality metric that 
indicate better quality when of higher value.}

\item{min_qual_variance}{numeric. Minimum proportion of selected quality 
variance addressed in filtering. Default 0.70}

\item{zcut}{A numeric value determining threshold Z-score for sd, mad, and 
mixture sub-criteria. Default 1.}

\item{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.}

\item{dip_thresh}{A numeric value determining dip test p-value threshold. 
Default 0.05.}

\item{plot}{logical. Should a plot be produced?}

\item{hist_breaks}{hist() breaks argument. Ignored if `plot=FALSE`.}
A logical, representing samples passing factor-based filter.
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.
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)