pp_seuratV3Integration: A wrapper function to quickly run fastMNN using...

In zzwch/convgene: This package is designed to conveniently convert gene between human and mouse.

Description

Run NormalizeData, CellCycleScoring, SelectIntegrationFeatures, RunFastMNN, RunUMAP/TSNE, FindClusters and FindMarkers. And save object_mnn and object_degs to xls and Rdata files.

Usage

pp_seuratV3Integration(
  object_list,
  genes_used = NULL,
  batch_by = "Batch",
  scale.factor = 1e+05,
  s.features = cc.genes$s.genes,
  g2m.features = cc.genes$g2m.gene,
  nfeatures = 2000,
  do.regress.cc = T,
  ndim = 20,
  skip_tsne = F,
  resolution = 0.5,
  save_object_prefix = NULL,
  save_degs_dir = "tables/",
  logfc.threshold = log(2),
  min.pct = 0.25,
  save_rdata_dir = "seuratData/",
  save_add.sys.time = F,
  ...
)

Arguments

object_list	a list of Seurat objects
genes_used	Set NULL to use the intersection of all Seurat objects.
batch_by	Attribute for splitting. Default is "Batch". (SplitObject)
scale.factor	Sets the scale factor for cell-level normalization. (NormalizeData)
s.features	A vector of features associated with S phase (CellCycleScoring)
g2m.features	A vector of features associated with G2M phase (CellCycleScoring)
nfeatures	Number of features to return (SelectIntegrationFeatures)
do.regress.cc	regress out cell cycle scores (ScaleData)
ndim	Number of dimensions to use for dimensionality reduction in multiBatchPCA. (batchelor::fastMNN)
skip_tsne	you may set TRUE to skip RunTSNE step for large dataset.
resolution	Value of the resolution parameter (FindClusters)
save_object_prefix	Set NULL to skip save files and FindAllMarker steps. Or a character setting the object prefix, e.g. AAA will get AAA_mnn and AAA_degs being returned.
save_degs_dir	save_object_prefix_degs.seurat_clusters.sys.time.xls will be written to here.
logfc.threshold	Limit testing to genes which show at least X-fold difference (log-scale) between the two groups of cells. (FindAllMarkers)
min.pct	only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. (FindAllMarkers)
save_rdata_dir	save_object_prefix_mnn.seurat.sys.time.Rdata will be written to here.
save_add.sys.time	whether to add sys.time to file names.
...	Extra parameters passed to IntegrateData

Value

seurat object if save_object_prefix is NULL, else saved files.

zzwch/convgene documentation built on July 11, 2021, 9:41 a.m.