getEDY: getEDY

Description Usage Arguments Details Value

View source: R/getEDY.R

Description

Detection of individuals with Extreme Downregulation of chromosome Y (EDY) from transcriptomic data

Usage

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getEDY(x, gender.var, male.key, gene.key, coef = 1.2, log = TRUE,
  group.var, control.key, experiment.type, ...)

Arguments

x

An ExpressionSet or RangedSummarizedExperiment from microarray or RNAseq experiments.

gender.var

A string indicating the name of the column in the table of phenotype (accessed by pData or colData) that contains the gender of the individuals.

male.key

A string indicating the symbol that idendtifies males (e.g., "male", "M", ...).

gene.key

A string indicating the name of the column that contains the Gene Symbol in the table of features (accessed by fData or rowData).

coef

Numerical. Value to consider an outlier when calling getEDY. Default correspond to 1.2 which keeps 5% of data in the normal case.

log

Logical. It is set to TRUE if the gene expression values are given in a logarithmic scale in the data set and FALSE otherwise. Default is TRUE.

group.var

A string indicating the name of the column that contains the information about whether the individual is case or control (accessed by pData or colData).

control.key

A string indicating the symbol that identifies control group (e.g., "control").

experiment.type

A string indicating whether the data set is a microarray or a RNAseq experiment

Details

To assess EDY, the function measures the relative expression of the entire chromosome Y with respect to the autosomes for each individual. For n probes (exons) in chromosome Y, with x{i} intensity (read counts) for the i-th probe, it computes y = 1/n · ∑log2(x{i}) as a measure of the average expression of chromosome Y (summation limits between i=1 and N). Likewise, for m probes in the autosomes, the function computes the mean expression of autosomes a = 1/m · ∑log2(x{i}) (summation limits between i=1 and M) [NOTE: for RNAseq data log2(x{i} + 1) is computed to avoid problems with zero counts]. The relative amount of an individual's Y expression with respect to the individual's autosomes is then Ry = y - a, and, in a population sample, the individual j is considered with EDY if

Ry{j} < median(Ry) - 1.2 · IQR(Ry)

where IQR is the inter-quartile range across the sample.

Value

A list containing 4 objects:


isglobal-brge/EDY documentation built on Jan. 24, 2020, 3:21 a.m.