ciberAMP: Perform joint expression and copy-number variation analyses...

In vqf/ciberAMP: mRNA and copy number data integrative algorithm.

Perform joint expression and copy-number variation analyses on a set of genes using a set of tumor samples.

Description

Perform joint expression and copy-number variation analyses on a set of genes using a set of tumor samples.

CiberAMP LUSC/HNSC example data (genes)

Usage

ciberAMP(
  genes = c(),
  cohorts = c(),
  writePath = NULL,
  pat.percentage = 0,
  pp.cor.cut = 0.6,
  norm.method = "geneLength",
  filt.method = "quantile",
  filt.qnt.cut = 0.25,
  filt.var.func = "IQR",
  filt.var.cutoff = 0.75,
  filt.eta = 0.05,
  filt.FDR.DEA = 0.05,
  filt.FC = 0.58,
  cna.thr = "Deep",
  exp.mat = NULL,
  cna.mat = NULL
)

data(ciberAMP)

Arguments

genes	Vector of approved queried genes symbols to be analyzed.
cohorts	Vector of TCGA cohorts IDs. See function all_tumors for a list of available tumors. If is left empty, CiberAMP will run on every cohort.
writePath	Path where results are stored. Defaults to the current folder.
pat.percentage	Minimum percentage of patients per group.
pp.cor.cut	Threshold to filter samples by AICC. Passed to 'TCGAanalyze_Preprocessing'.
norm.method	Method of normalization, such as 'gcContent' or 'geneLength' (default). Passed to 'TCGAanalyze_Normalization'.
filt.method	Method of filtering, such as 'quantile' (default), 'varFilter', 'filter1', 'filter2'.
filt.qnt.cut	Threshold selected as mean for filtering. Defaults to 0.25.
filt.var.func	Filtering function. Defaults to 'IQR'. See 'genefilter' documentation for available methods.
filt.var.cutoff	Threshold for 'filt.var.funct'.
filt.eta	Parameter for 'filter1'. Defaults to 0.05.
filt.FDR.DEA	Threshold to filter differentially expressed genes according their adjusted p-value. Passed to 'TCGAanalyze_DEA'.
filt.FC	Minimum log2(FC) value to considered a gene as differentially expressed. Defaults to 1.
cna.thr	Threshold level for copy-number variation analysis. Can be 'Deep', 'Shallow' or 'Both'. 'Deep', to consider homozygous deletions and high-level broad amplifications. 'Shallow', to consider hemyzygous deletions and low-level focal amplifications. 'Both', to consider deep and shallow amplifications/deletions in the same group: one group -> deep + shallow amp; second group -> deep + shallow del.
exp.mat	Custom normalized RNAseq counts expression matrix of only tumors. Defaults to 'NULL'.
cna.mat	Custom copy-number analysis matrix of only tumors. Defaults to 'NULL'.

Format

An object of class "cross"; see read.cross.

Value

List containing three data frames: 1 - SCNA-mRNA correlations for queried genes 2 - SCNA-mRNA correlations for Cancer Census genes (COSMIC) | Known oncodriver/TSGs. 3 - SCNA overlapping between queried and CGC genes.

vqf/ciberAMP documentation built on April 12, 2022, 12:45 p.m.