Description Usage Arguments Details Value
Detection of individuals with Extreme Downregulation of chromosome Y (EDY) from transcriptomic data
1 2 |
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 |
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 |
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 |
group.var |
A string indicating the name of the column that contains the
information about whether the individual is case or control (accessed by
|
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 |
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.
A list containing 4 objects:
EDY
: a factor with two levels, NO
and YES
,
that indicates whether the individual has EDY or not.
EDYcontinuous
: a vector with individual relative expression
of chromosome Y with regard the autosomal genes.
threshold
: a number indicating the threshold from which down
an individual is considered to have EDY.
eSet
or RangedSummarizedExperiment
: an ExpressionSet
or RangedSummarizedExperiment that contains only males from the initial
data set. It contains a new column in pData
or colData
containing the EDY status of each individual.
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