findCells_OG: findCells

In plantformatics/Socrates: Analysis of scATAC-seq data

findCells

Description

This function filters cells based on read-depth using obj mixture of user thresholds and obj spline- fitting algorithm.

Usage

findCells(
  obj,
  set.tn5.cutoff = NULL,
  min.cells = 1000,
  max.cells = 15000,
  min.tn5 = 1000,
  filt.org = F,
  org.filter.thresh = 0.8,
  filt.tss = T,
  tss.min.freq = 0.2,
  tss.z.thresh = 2,
  filt.frip = T,
  frip.min.freq = 0.2,
  frip.z.thresh = 2,
  doplot = F,
  prefix = NULL
)

Arguments

obj	Object output from buildMetaData. Required.
set.tn5.cutoff	Override spline fitting to set minimum tn5 count per cell. Defaults to NULL.
min.cells	Lower limit on the number of identified cells. Defaults to 1000.
max.cells	Upper limit on the number of identified cells. Defaults to 15000.
min.tn5	Lower threshold for the minimum number of Tn5 integration sites for retaining obj barcode. Defaults to 1000.
filt.org	Logical. Whether or not to filter barcodes on based on proportion Tn5 sites occuring in an organelle. Defaults to FALSE. Expects organelles built off meta
org.filter.thresh	Remove cells with an organelle ratio (Organalle/Total_reads) greater than N
filt.tss	Logical. Whether or not to filter barcodes on based on proportion Tn5 sites over- lapping gene TSS. Defaults to TRUE. Filtering barcodes with this parameter is highly recommended.
tss.min.freq	Float. Minimum frequency of Tn5 sites near TSSs. Defaults to 0.2.
tss.z.thresh	Numeric. Z-score threshold to remove barcodes below the mean. Defeaults to 3 standard deviations (3).
filt.frip	Logical. Whether or not to filter barcodes based on the proportion of Tn5 sites over- lapping bulk ACRs. Defaults to TRUE. Using this filter is highly recommended.
frip.min.freq	Float. Minimum frequency of Tn5 sites within ACRs. Defaults to 0.2.
frip.z.thresh	Numeric. Z-score threshold to remove barcodes with values below X standard deviations from the mean. Defaults to 3.
doplot	Logical. Whether or not to plot the density scatter plots for tss/frip values.
prefix	Character. Prefix output name for plots. If changed from the default (NULL), this will save the images to disk as obj PDF.

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.