Read10X_RemoveDoublets_Norm: A Read10X_RemoveDoublets_Norm Function

In parveendabas/SCA: What the Package Does (One Line, Title Case)

A Read10X_RemoveDoublets_Norm Function

Description

This function allows you to Read 10X data, remove doublets, perform normalizationa and identify variable genes.

Usage

Read10X_RemoveDoublets_Norm(
  matrix.DIR,
  saveDIR,
  Sample,
  Doublet.DIR,
  Species = "hsa",
  DoubletAlgo = "DoubletFinder",
  mincells = 3,
  mingenes = 500,
  mtpercent = 20,
  rbpercent = 50,
  FeatureUseCount = 2500,
  PCAnum = 10,
  resClus = 0.5,
  plots = TRUE,
  save = TRUE
)

Arguments

matrix.DIR	Path to 10X directory
saveDIR	Path to save Quality plots and RDS data.
Sample	Sample Name.
Doublet.DIR	Path to Doublet.DIR directory (List of cells already called doublets)
Species	Species Name. Valid options are hsa or mmu
DoubletAlgo	Algorithm(s) used for doublet detection. Valid options are "DoubletFinder" for DoubletFinder and "DoubletDeconFinder" for DoubletFinder+DoubletDecon
mincells	Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff.
mingenes	Include cells where at least this many features are detected.
mtpercent	Include cells reporting at most this much mitochondrial transcript percentage.
rbpercent	Include cells reporting at most this much ribosomal transcript percentage.
FeatureUseCount	Number of features to select as top variable features; only used when selection.method is set to 'dispersion' or 'vst'
PCAnum	Number of PCs to be used
resClus	Resolution to be used for clustering
plots	Save QC plots
save	Save RDS Seurat object

Examples

Read10X_RemoveDoublets_Norm()

parveendabas/SCA documentation built on Sept. 19, 2022, 8:31 a.m.