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Sample count condition for MS analyses

ms_condition.Rd

The number of non-missing samples per treatment group determine whether it can be used in subsequent analyses.

Usage

ms_condition(data, treatment, control = NULL, condition = c("VC", "MRC", "MC"))

Arguments

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.

Value

A logical vector of length equal to the number of rows in data, indicating which observations are kept and which are to be removed.

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.

See also

Other Mass Spectrometry functions: ms_plot, ms_process(), ms_summarize(), ms_top()

Author

Derek Chiu

Examples

# 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")
#> [1] FALSE  TRUE  TRUE FALSE FALSE FALSE
ms_condition(A, treatment = c("X19", "X5"), condition = "MRC")
#> [1] FALSE  TRUE  TRUE  TRUE  TRUE  TRUE
ms_condition(A, treatment = c("X19", "X5"), condition = "MC")
#> [1] TRUE TRUE TRUE TRUE TRUE TRUE

# Control ends in "_1", Treatments ends in "_2", "_3"
ms_condition(A, treatment = c("_2", "_3"), control = "_1", condition = "VC")
#> [1] FALSE FALSE  TRUE FALSE FALSE FALSE
ms_condition(A, treatment = c("_2", "_3"), control = "_1", condition = "MRC")
#> [1] FALSE FALSE  TRUE  TRUE FALSE FALSE
ms_condition(A, treatment = c("_2", "_3"), control = "_1", condition = "MC")
#> [1] FALSE FALSE  TRUE  TRUE FALSE  TRUE