Description Usage Arguments Details Value Examples
View source: R/permutation_functions.R
Apply permutation on MFA or Zhang results to obtain p-values of 1 of the components. The function asks for a CSresult object which is returned by CSanalysis. The CSpermute function will return the same CSresult object with added information such as p-values. If asked, the CSpermute function will also draw a volcanoplot and/or histograms of the p-values. If you simply want to redraw these plots, simply use the returned CSresult object by CSpermute again in the CSpermute function. If the number of permutations was not changed, this will prevent the entire permutation analysis from being redone.
1 2 3 4 5 6 | CSpermute(querMat, refMat, CSresult, B = 500, mfa.factor = NULL,
method.adjust = "none", verbose = TRUE, which = c(1, 3),
cmpd.hist = NULL, color.columns = NULL, labels = TRUE,
plot.type = "device", basefilename = NULL, MultiCores = FALSE,
MultiCores.number = detectCores(logical = FALSE), MultiCores.seed = NULL,
save.permutation = TRUE)
|
querMat |
Query matrix (Rows = genes and columns = compounds). |
refMat |
Reference matrix |
CSresult |
A CSresult class object. |
B |
Number of permutations. |
mfa.factor |
If permuting a CSmfa result, mfa.factor will decide of which factor the p-values should be computed. If |
method.adjust |
Correction method of multiplicity adjusted p-values: "none", "holm", "hochberg", "hommel", "bonferroni", "BH", "BY" or "fdr". (Raw p-values are also always provided) |
verbose |
If |
which |
Choose which plot to draw:
|
cmpd.hist |
Reference index vector which decides which reference compounds are plotted for the histogram distribution under null hypothesis ( |
color.columns |
Option to color the compounds on the volcano plot ( |
labels |
Boolean value (default=TRUE) to use row and/or column text labels in the volcano plots ( |
plot.type |
How should the plots be outputted? |
basefilename |
Directory including filename of the graphs if saved in pdf files |
MultiCores |
Logical value parallelisation should be used for permutation. |
MultiCores.number |
Number of cores to be used for |
MultiCores.seed |
Seed to be used for |
save.permutation |
Logical value if the scores (CLoadings, CRankingScores, ZG Scores) of each permuted data set should be saved (default= |
IMPORTANT! For MFA, CSpermute
should only be used to compute the p-values of the Component in which the structure (loadings) of the queries is the strongest.
This because in each permutation the factor with the highest average query loadings will be chosen.
The ability to compute p-values of other factors (in which the query set also increased loadings) will be added in a later release.
Returns the same CSresult-class
object with added p-values to the CS slot and added information to the permutation.object slot. This CSresult can be reused in CSpermute to redraw the plots without calculation.
1 2 3 4 5 6 |
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