README.md

In CharleneZ95/infercnvPlus: Enhanced 'infercnv' package

infercnvPlus

Desciption

Enhanced "infercnv" package.

Input

expression data: a matrix of Genes(rows) X Cells(columns). 10X counts data or Smart-seq2 TPM values. | | CCCTCCTAGCAGCGTA | GTCTCGTCATCCTTGC | TCAGATGGTCATTAGC | ATTCTACCATCTATGG | GACGTGCGTAGCTGCC | | ---- | :----: | :----: | :----: | :----: | :----: | | AL627309.1 | 0 | 0 | 0 | 0 | 0 | | AL669831.5 | 0 | 0 | 2 | 0 | 0 | | LINC00115 | 1 | 0 | 0 | 0 | 0 | | FAM41C | 0 | 0 | 0 | 0 | 0 | | NOC2L | 1 | 0 | 0 | 1 | 0 |

genomic_pos： a "data.frame" contains genomic coordinates for genes. | | CHR | START | STOP | | :---- | :----: | :----: | :----: | | RP11-34P13.3 | 1 | 29554 | 31109 | | FAM138A | 1 | 34554 | 36081 | | OR4F5 | 1 | 69091 | 70008 | | RP11-34P13.7 | 1 | 89295 | 133723 | | RP11-34P13.8 | 1 | 89551 | 91105 |

Usage

Run infercnvPlus using built-in data

library(infercnvPlus)

# Load built-in data (10X counts)
data(expr, genomic_pos, ref_obs, package = "infercnvPlus")

# Data tranforming
## For 10X counts data 
expr_tr <- umi_to_log2tpm(expr)

## For Smart-seq2 TPM values
expr_tr <- log2(expr + 1)

# Calucate cnv score
cnv_obj <- inferCNV(data = expr_tr,
                    gene_pos = genomic_pos,
                    cutoff = 0.1, # use 1 for smart-seq, 0.1 for 10x-genomics
                    reference_obs = ref_obs,
                    window_size = 101,
                    out_path = "output_dir", # dir is auto-created for storing outputs
                    noise_filter = NULL,
                    vis_bounds = "-1,1")

# Cluster cells and visualize
cnv_obj <- visualCNV(data = cnv_obj,
                     cutree_k = 2,
                     out_file = "plot_cnv.png")

# Extract cells from the specific subtrees
cnv_obj <- extractCells(data = cnv_obj,
                        subtrees = 2,
                        lab_to_rm = "ref")

# Get cell barcode
cells <- cnv_obj$target

Output figure

FAQ

How to generate a genomic positions file from a GTF file?

genomic_pos <- gtf_to_position(gtf = "path/to/gtf", out_file = "genomic_positions.txt", out_path = "./")

How to convert a Seurat(v3) object to matrix for inferCNV?

expr_tr <- importSrat(obj, slot = "counts", assay = "RNA", log2tpm_tr = TRUE)

CharleneZ95/infercnvPlus documentation built on April 9, 2020, 3:40 a.m.