R/iGC.R

In iGC: An integrated analysis package of Gene expression and Copy number alteration

#' iGC: an integrated analysis package of gene expression and copy number
#' alteration
#'
#' The iGC package is used to identify CNA-driven differentially expressed
#' genes. The iGC package provides four categories of important functions:
#' `create_sample_desc`, `create_gene_ex`, `create_gene_cna` and
#' `find_cna_drive_gene`.
#'
#' @section create_sample_desc: The create_sample_desc function is provided for
#'   creating a sample description table containing all required inputs.
#'
#'
#' @section create_gene_exp function: The create_gene_exp function is used to
#'   rearrange the input gene expression files into a gene expression list of
#'   entire samples.
#'
#' @section create_gene_cna function: The create_gene_cna function maps CNA data
#'   to human genes and then defines the mapped human genes as CN gain or loss
#'   based on the CN threshold, whose default values are set as 2.5 for gain and
#'   1.5 for loss. These mapped genes will be assigned values in +1, -1 or 0,
#'   where +1 stands for CNA-gain, -1 stands for CNA-loss and 0 stands for
#'   neutral.
#'
#' @section find_cna_driven_gene function: The find_cna_driven_gene function
#'   identifies CNA-driven differentially expressed genes. The input mapped
#'   genes remain for further analyses if its ratio of the number of CN changed
#'   samples, CNA-gain (G) or CNA-loss (L), to the number of total samples is
#'   larger than a given threshold. Here the default setting is that only genes
#'   showing CNAs in at least 20% of the samples will be analyzed further. Then,
#'   statistical tests, T-test and Wilcoxon rank sum test, are performed in the
#'   GE level by classifying the samples as G and L plus Nertral (N) groups or L
#'   and G plus N groups, depending on the CN of the interested gene increases
#'   or decreases.
#'
#' @docType package
#' @name iGC
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