Description Usage Arguments Value
View source: R/RNASeqUtilities.R
Apply DEG analysis to voom normalised data for a specific model and coefficients.
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voomDat |
Eset of voom normalised data which must include the design. This is the output of voom function in limma. |
coefs |
Vector of coefficients to test. They must map to a coefficient in the design matrix in 'voomDat'. |
doRandomEffect |
Boolean indicating whether there is a random effect in the model. If so then 'duplicateCorrelation' function is run based on 'blocker'. The blocking factor must be identified by 'blocker' parameter. |
blocker |
Vector showing factor of random effect. It is only used if doRandomEffect is TRUE. |
labels |
Vector of character strings that labels each coefficient being tested. This allows for more human readable labels than the lmFit coefficients. Labels must map one to one to 'coefs'. |
doWrite |
Boolean indicating whether to write the random correlation and fitted model to file defined in 'rdaPath'. Useful because computation time can be prohibitive when fitting model. |
doRead |
Boolean indicating whether to read random corrleation and fitted model from file defined in 'rdaPath'. Data must have been previously saved with 'doWrite' parameter. |
rdaPath |
Character string defining full path where rda object will be stored or read. Must be defined if 'doWrite' or 'doRead' are TRUE. |
List of DEG results. Each element in list corresponds to the results for the matching coefficients in 'coefs'.
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