ms_condition | R Documentation |
The number of non-missing samples per treatment group determine whether it can be used in subsequent analyses.
ms_condition(data, treatment, control = NULL, condition = c("VC", "MRC", "MC"))
data |
The data matrix with rows as observations, columns as variables |
treatment |
A character vector indicating how different treatment groups are coded. Regular expression is used on the column names to find all relevant treatment variables. |
control |
Optionally specify a character string indicating the control group if it exists. Regular expression is used on the column names to find all relevant control variables. |
condition |
Either one of "VC" (default), "MRC", or "MC". See details. |
The Variance Condition (VC) (default) requires at least two non-missing samples in each of the treatment groups. A rudimentary estimate of variance is possible when this phenomenon exists. The Minimum Reasonable Condition (MRC) requires all treatment groups to have at least one non-missing sample and one treatment group to have at least two non-missing samples. Equal variance assumption is used in the case of MRC. Finally, the Minimum Condition (MC) requires at least one non-missing sample in each of the treatment groups. MC is not generally suggested in practice.
Additionally, if there are controls, they are handled by MC.
A logical vector of length equal to the number of rows in
data
, indicating which observations are kept and which are to be
removed.
Derek Chiu
Other Mass Spectrometry functions:
ms_plot
,
ms_process()
,
ms_summarize()
,
ms_top()
# Example data matrix with some missing sample values
g <- c("X5", "X19")
r <- c("1", "2", "3")
col.nm <- sort(apply(expand.grid(g, r), 1, paste, collapse = "_"))
A <- matrix(c(seq_len(36)), ncol = 6, byrow = FALSE, dimnames = list(NULL, col.nm))
A[c(1, 21, 26, 7, 17, 8, 23, 4, 16, 19, 5, 25, 12, 18, 24)] <- NA
# Two treatment experimental design
ms_condition(A, treatment = c("X19", "X5"), condition = "VC")
ms_condition(A, treatment = c("X19", "X5"), condition = "MRC")
ms_condition(A, treatment = c("X19", "X5"), condition = "MC")
# Control ends in "_1", Treatments ends in "_2", "_3"
ms_condition(A, treatment = c("_2", "_3"), control = "_1", condition = "VC")
ms_condition(A, treatment = c("_2", "_3"), control = "_1", condition = "MRC")
ms_condition(A, treatment = c("_2", "_3"), control = "_1", condition = "MC")
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