topgenes.corCluster_log: Compute the correlation matrix for the correlation of the two...

In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

Compute the correlation matrix for the correlation of the two studies' tissues (columns) after they have been transformed with log

Description

Compute the correlation matrix for the correlation of the two studies' tissues (columns) after they have been transformed with log

Usage

topgenes.corCluster_log(a, b, filta = NA, same = FALSE, filtb = NA,
  top = 0, use = "pairwise.complete.obs", method = "pearson",
  nameA = deparse(substitute(a)), nameB = deparse(substitute(b)),
  cleanInfinite = TRUE, pseudocount = 1)

Arguments

a	data.frame with expression data for the first study
b	data.frame with expression data for the second study
filta	character vector or positive integer vector. colnames or indices of the columns to consider for the first study.
same	boolean. Default:FALSE. Whether the tissues (columns) from the second study should be identical to the first study.
filtb	character vector or positive integer vector. colnames or indices of the columns to consider for the second study.
top	positive integer. Number of genes to consider for the analysis; if 0 (default), all genes are considered.
use	character string expliciting how missing values should be handled. can be either "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs" (default). To fasten the process if there is no missing value, use "everything".
method	character string. Method for base::cor, either "pearson", "spearman" or "kendall".
nameA	character string to use for identifying the first study
nameB	character string to use for identifying the second study
cleanInfinite	boolean. Default: TRUE. whether to use clean.infinite to handle log(0)
pseudocount	numeric. Default: 1. Pseudocount in case for log(x+pseudocount) when clean.infinite is not used for log(0)

Value

a matrix with the correlation of the columns of the two data.frames once log2-transformed

barzine/barzinePhdR documentation built on Nov. 23, 2024, 8:54 p.m.