Description Usage Arguments Value Examples

View source: R/prot_p_adjust.R

Given data frame or a list of matrices with a column containing p-values, adds one or more columns containing p-values adjusted using one or more methods.

1 2 | ```
prot.p.adjust(coefmatlist, method = "fdr", pcol = "pval", qname = "qval",
Tcol = NULL, threshold_excess1 = 1e-90)
``` |

`coefmatlist` |
Either a data frame containing a column with p-values or a list of such matrices. A column with T-values is also necessary when |

`method` |
Correction method. Can be abbreviated. Defaults to |

`pcol` |
A character string or numeric index indicating the column containing the p-values. Defaults to |

`qname` |
A character string indicating the name that will be given to the column containing the q-values. Defaults to |

`Tcol` |
Only needed when |

`threshold_excess1` |
A numeric value between 0 and 1 indicating the threshold at which correcting for an excess in p-values close to 1 should be performed. This is sometimes needed when a null distribution needs to be fitted. Note that the method still accounts for the total number of p-values when performing this correction. Only if there is, according to a binomial test, a significant enrichment of p-values above an automatically determined cut-off at the |

Depending on the input, either a data frame or a list of data frames with an extra numeric column containing corrected p-values.

1 2 3 4 5 6 7 8 9 | ```
#Create a contrast matrix L for investigating whether all 10 pairwise contrasts between conditions conc6A, conc6B, conc6D and conc6E differ from zero:
L <- makeContrast(contrasts=c("conc6B-conc6A","conc6C-conc6A","conc6D-conc6A","conc6E-conc6A","conc6C-conc6B","conc6D-conc6B","conc6E-conc6B","conc6D-conc6C","conc6E-conc6C","conc6E-conc6D"),
levels=c("conc6A","conc6B","conc6C","conc6D","conc6E"))
#Load the protLM object protmodel:
protmodel <- data(modelRRCPTAC, package="MSqRob")
#Test the contrast L:
protvalues <- test.protLMcontrast(protmodel,L)
#Adjust the p-values by Benjamini-Hochberg FDR:
protvalues <- prot.p.adjust(protvalues)
``` |

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