pp_fastMNN: 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_fastMNN(
  object_list,
  genes_used = NULL,
  batch_by = "Batch",
  scale.factor = 1e+05,
  s.features = cc.genes$s.genes,
  g2m.features = cc.genes$g2m.gene,
  assay = c("RNA", "SCT"),
  nfeatures = 2000,
  integration_features = NULL,
  remove_ccgenes_by_cor = T,
  cc_cor_th = 0.3,
  mnn_d = 20,
  seed = 666,
  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. Calculated in RNA assay. (NormalizeData)
s.features	A vector of features associated with S phase. Calculated in RNA assay. (CellCycleScoring)
g2m.features	A vector of features associated with G2M phase. Calculated in RNA assay. (CellCycleScoring)
assay	which assay to be used for integration. default RNA.
nfeatures	Number of features to return (SelectIntegrationFeatures)
integration_features	if NULL use nfeatures, else use these feature for fastMNN
remove_ccgenes_by_cor	whether to exclude cell cycle-related genes using correlation method.
cc_cor_th	feature genes with correlation coefficient larger than this threshold will be removed.
mnn_d	Number of dimensions to use for dimensionality reduction in multiBatchPCA. (batchelor::fastMNN)
seed	random seed for 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 batchelor::fastMNN.

Value

seurat object if save_object_prefix is NULL, else saved files.

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