inferCNV: Infer CNV changes given a matrix of RNASeq counts. Output a...
In CharleneZ95/infercnvPlus: Enhanced 'infercnv' package

Infer CNV changes given a matrix of RNASeq counts. Output a pdf and matrix of final values.

inferCNV(
  data = NULL,
  gene_pos = NULL,
  cutoff = NULL,
  reference_obs,
  window_size = 101,
  out_path = "output_dir",
  contig_tail = NULL,
  noise_filter = NULL,
  vis_bounds = "-1,1"
)

`data`	expression matrix (genes X cells), assumed to be log2(TPM+1).
`gene_pos`	The gene ordering file provides the chromosomal location for each gene. Simply providing the gene name, chromosome, and gene span.
`cutoff`	cut-off for the average expression of genes to be used for CNV inference.
`reference_obs`	column names of the subset of cells (data's columns) that should be used as references. If not given, the average of all cells will be the reference.
`window_size`	length of the window for the moving average (smoothing). Should be an odd integer.
`out_path`	the path to what to save the pdf as. The raw data is also written to this path but with the extension .txt .
`contig_tail`	length of the tail removed from the ends of contigs.
`noise_filter`	the minimum difference a value can be from the average reference in order for it not to be removed as noise.
`vis_bounds`	Used as upper and lower bounds for values in the visualization. Should be given in the form of '-1,1' (lower bound, upper bound).

Returns an 'infercnv' object including: 1. CNV matrix before visualization. 2. CNV matrix after denoise and outlier removal for visualization. 3. Chromosome order. 4. Names of cells in reference groups.

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