compute_t_tests: xxxxxx

In prostarproteomics/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

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Description

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Usage

compute_t_tests(obj, contrast = "OnevsOne", type = "Student")

Arguments

obj	A matrix of quantitative data, without any missing values.
contrast	Indicates if the test consists of the comparison of each biological condition versus each of the other ones (contrast=1; for example H0:"C1=C2" vs H1:"C1!=C2", etc.) or each condition versus all others (contrast=2; e.g. H0:"C1=(C2+C3)/2" vs H1:"C1!=(C2+C3)/2", etc. if there are three conditions).
type	xxxxx

Value

A list of two items : logFC and P_Value; both are dataframe. The first one contains the logFC values of all the comparisons (one column for one comparison), the second one contains the pvalue of all the comparisons (one column for one comparison). The names of the columns for those two dataframes are identical and correspond to the description of the comparison.

Author(s)

Florence Combes, Samuel Wieczorek

Examples

data(Exp1_R25_prot, package="DAPARdata")
obj <- Exp1_R25_prot[seq_len(1000)]
level <- 'protein'
metacell.mask <- match.metacell(GetMetacell(obj), c("Missing POV", "Missing MEC"), level)
indices <- GetIndices_WholeMatrix(metacell.mask, op = ">=", th = 1)
obj <- MetaCellFiltering(obj, indices, cmd = "delete")
ttest <- compute_t_tests(obj$new)

prostarproteomics/DAPAR documentation built on Oct. 11, 2024, 12:03 p.m.