xsharedDistrib: Compute and compare the breadth of expression of two datasets...
In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

xsharedDistrib

R Documentation

Compute and compare the breadth of expression of two datasets and send back the resuls as a list of data.frames

Compute and compare the breadth of expression of two datasets and send back the resuls as a list of data.frames

xsharedDistrib(DF1, DF2, omit.zero = TRUE, threshold = 0,
  strict = FALSE, simplify = TRUE, Lims = c(1, 3, 10, 12),
  lapse = 3)

`DF1`	numeric data.frame comprising the expression data of the first study.
`DF2`	numeric data.frame comprising the expression data of the second study.
`omit.zero`	boolean. Default: TRUE. Whether the genes which do not reach the minimal expression threshold in any tissue should be stripped from the output.
`threshold`	numeric. Default: 0. Minimal level of expression to be considered as expressed.
`strict`	boolean. Default:FALSE. Whether if only strict equality between the breadth of expression of each gene between the two studies should be considered or if the "lapse" argument should be used to define 'similar' cases as well.
`simplify`	boolean. Default: TRUE. Whether to focus only on the most extreme breadth of expression. "Expressed in all" or "nearly in all" might be more descriptive than "expressed in 5" versus "expressed in 6".
`Lims`	a length-4 numeric vector. Default: c(1,3,10,12). When the analysis is in the "simplify" mode, it allows to delimit two ranges of expression breadth to compare between the two studies.
`lapse`	positive integer. Default: 3. Allow to relax constraints on perfect equality of breadth for the genes between the two studies. A "similar" class is created. The lapse allows to define which level of similarity is acceptable. e.g. if lapse=3, all genes that have a breadth of expression that varies at most of 3 are considered to have similar breadth.