Function returns a named vector with scores [-1,1]. Names are genes. Values are scores that indicate whether a gene is DE based on FC and z criteria.
1 2 | E3GetDEScores(sampledata, sampleA, refsamples, scorefun = E3DEscore,
rankrescale = TRUE, shiftval = 0.1)
|
sampledata |
- list with expression, expression.low, expression.high tables |
sampleA |
- character string. The sample for which the signature is made |
refsamples |
- character vector. Reference samples to which sampleA is compared. |
scorefun |
- function. This function should accept two arguments (fc and z) and return a numeric score. |
rankrescale |
- logical. Set TRUE to penalize scores in an ad-hoc way for genes that have a high score but lower fc or lower z than many other genes. |
shiftval |
- numeric. Used when computing FC to avoid division by zero. return - a vector with gene names and then a score [0,1] Score 1 means the gene is DE wrt all samples in groupB |
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