IBRIDGE_overlaps: IBRIDGE_Overlaps Integrates bulk with single-cell (or cell...

In tolgaturan-github/IBRIDGE: IBRIDGE integrates bulk and single-cell datasets to profile granular heterogeneity of TIME, acting as a 'bridge' between data types.

IBRIDGE_Overlaps Integrates bulk with single-cell (or cell line) gene expression data and identifies features that can classfy cells into "inflamed" and "cold" bins.

Description

IBRIDGE_Overlaps Integrates bulk with single-cell (or cell line) gene expression data and identifies features that can classfy cells into "inflamed" and "cold" bins.

Usage

IBRIDGE_overlaps(
  seu1,
  type = "ens",
  cohort = c("ACC", "BLCA", "CESC", "CHOL", "COAD", "ESCA", "GBM", "HNSC", "KICH",
    "KIRC", "KIRP", "LGG", "LIHC", "LUAD", "LUSC", "MESO", "OV", "PAAD", "PRAD", "READ",
    "SARC", "SKCM", "STAD", "THCA", "UCEC", "UCS"),
  norm_method = "SCTransform"
)

Arguments

seu1	Output of UMI count matrix normalized by Seurat workflows.
type	type of gene identifier the dataset has. "ens" for ensembl IDs and "gene" for HUGO gene exymbols. Defaults to "ens"
cohort	one of 28 solid tumor cohorts from TCGA database. The cancer cohort from which the single-cell gene expression dataset is generated.
norm_method	"SCTransform" or "NormalizeData". Defaults to "SCTransform"

Value

list of 2 elements. One for "inflamed" and one for "cold" features.

Author(s)

Tolga Turan, [e-mail]

References

http://github.com/tolgaturan-github/IBRIDGE

Examples

IBRIDGE_features<-IBRIDGE_overlaps(seu1, "LUAD", "SCTransform")

tolgaturan-github/IBRIDGE documentation built on July 30, 2023, 12:08 p.m.