mmcm.resamp: The permuted modified maximum contrast method
In mmcm: Modified Maximum Contrast Method

Description Usage Arguments Details Value References See Also Examples

View source: R/mmcm.resamp.R

This function gives P-value for the permuted modified maximum contrast method.

1 2	mmcm.resamp(x, g, contrast, alternative = c("two.sided", "less", "greater"), nsample = 20000, abseps = 0.001, seed = NULL)

`x`	a numeric vector of data values
`g`	a integer vector giving the group for the corresponding elements of x
`contrast`	a numeric contrast coefficient matrix for permuted modified maximum contrast statistics
`alternative`	a character string specifying the alternative hypothesis, must be one of "two.sided" (default), "greater" or "less". You can specify just the initial letter.
`nsample`	specifies the number of resamples (default: 20000)
`abseps`	specifies the absolute error tolerance (default: 0.001)
`seed`	a single value, interpreted as an integer; see `set.seed()` function. (default: NULL)

mmcm.resamp performs the permuted modified maximum contrast method that is detecting a true response pattern under the unequal sample size situation.

Y_ij (i = 1, 2, ...; j = 1, 2, ..., n_i) is an observed response for j-th individual in i-th group.

C is coefficient matrix for permuted modified maximum contrast statistics (i x k matrix, i: No. of groups, k: No. of pattern).

C = (c_1, c_2, ..., c_k)^T

c_k is coefficient vector of k-th pattern.

c_k = (c_k1, c_k2, ..., c_ki)^T (sum from i of c_ki = 0)

M_max is a permuted modified maximum contrast statistic.

Ybar_i = (sum from j of Y_ij) / n_i, Ybar = (Ybar_1, Ybar_2, ..., Ybar_i, ..., Ybar_a)^T (a x 1 vector), M_k = c_k^t Ybar / (c_k^t c_k)^(1/2),

M_max = max(M_1, M_2, ..., M_k).

Consider testing the overall null hypothesis H_0: μ_1=μ_2=…=μ_i, versus alternative hypotheses H_1 for response petterns (H_1: μ_1<μ_2<…<μ_i, μ_1=μ_2<…<μ_i, μ_1<μ_2<…=μ_i). The P-value for the probability distribution of M_max under the overall null hypothesis is

P-value = Pr(M_max > m_max | H0)

m_max is observed value of statistics. This function gives distribution of M_max by using the permutation method, follow algorithm:

1. Initialize counting variable: COUNT = 0. Input parameters: NRESAMPMIN (minimum resampling count, we set 1000), NRESAMPMAX (maximum resampling count), and epsilon (absolute error tolerance).

2. Calculate m_max that is the observed value of the test statistic.

3. Let y_ij(r) donate data, which are sampled without replacement, and independently, form observed value y_ij. Where, (r) is suffix of the resampling number (r = 1, 2, ...).

4. Calculate m(r)_max from y_ij(r). If m(r)_max > m_max, then increment the counting variable: COUNT = COUNT + 1. Calculate approximate P-value hat-p(r) = COUNT / r, and the simulation standard error [hat-p(r) (1 - hat-p(r)) / r]^(1/2).

5. Repeat 3–4, while r > 1000 and 3.5 SE(hat-p(r)) < epsilon (corresponding to 99% confidence level), or NRESAMPMAX times. Output the approximate P-value hat-p(r).

`statistic`	the value of the test statistic with a name describing it.
`p.value`	the p-value for the test.
`alternative`	a character string describing the alternative hypothesis.
`method`	the type of test applied.
`contrast`	a character string giving the names of the data.
`contrast.index`	a suffix of coefficient vector of the kth pattern that gives permuted modified maximum contrast statistics (row number of the coefficient matrix).
`error`	estimated absolute error and,
`msg`	status messages.

Nagashima, K., Sato, Y., Hamada, C. (2011). A modified maximum contrast method for unequal sample sizes in pharmacogenomic studies Stat Appl Genet Mol Biol. 10(1): Article 41. http://dx.doi.org/10.2202/1544-6115.1560

Sato, Y., Laird, N.M., Nagashima, K., et al. (2009). A new statistical screening approach for finding pharmacokinetics-related genes in genome-wide studies. Pharmacogenomics J. 9(2): 137–146. http://www.ncbi.nlm.nih.gov/pubmed/19104505

mmcm.mvt

## Example 1 ##
#  true response pattern: dominant model c=(1, 1, -2)
set.seed(136885)
x <- c(
  rnorm(130, mean =  1 / 6, sd = 1),
  rnorm( 90, mean =  1 / 6, sd = 1),
  rnorm( 10, mean = -2 / 6, sd = 1)
)
g <- rep(1:3, c(130, 90, 10))
boxplot(
  x ~ g,
  width = c(length(g[g==1]), length(g[g==2]), length(g[g==3])),
  main  = "Dominant model (sample data)",
  xlab  = "Genotype", ylab="PK parameter"
)

# coefficient matrix
# c_1: additive, c_2: recessive, c_3: dominant
contrast <- rbind(
  c(-1, 0, 1), c(-2, 1, 1), c(-1, -1, 2)
)
y <- mmcm.resamp(x, g, contrast, nsample = 20000, abseps = 0.01, seed = 5784324)
y

## Example 2 ##
#  for dataframe
#  true response pattern: pos = 1 dominant  model c=( 1,  1, -2)
#                               2 additive  model c=(-1,  0,  1)
#                               3 recessive model c=( 2, -1, -1)
set.seed(3872435)
x <- c(
  rnorm(130, mean =  1 / 6, sd = 1),
  rnorm( 90, mean =  1 / 6, sd = 1),
  rnorm( 10, mean = -2 / 6, sd = 1),
  rnorm(130, mean = -1 / 4, sd = 1),
  rnorm( 90, mean =  0 / 4, sd = 1),
  rnorm( 10, mean =  1 / 4, sd = 1),
  rnorm(130, mean =  2 / 6, sd = 1),
  rnorm( 90, mean = -1 / 6, sd = 1),
  rnorm( 10, mean = -1 / 6, sd = 1)
)
g   <- rep(rep(1:3, c(130, 90, 10)), 3)
pos <- rep(c("rsXXXX", "rsYYYY", "rsZZZZ"), each=230)
xx  <- data.frame(pos = pos, x = x, g = g)

# coefficient matrix
# c_1: additive, c_2: recessive, c_3: dominant
contrast <- rbind(
  c(-1, 0, 1), c(-2, 1, 1), c(-1, -1, 2)
)

mmcmtapply <- function(r) {
  mmcm.resamp(
    xx$x[xx$pos==r[1]], xx$g[xx$pos==r[1]],
    contrast, nsample = 10000, abseps = 0.01, seed = 5784324+as.numeric(r[1])
  )
}
y <- tapply(xx$pos, xx$pos, mmcmtapply)
yy <- data.frame(
  Pos      = as.vector(names(y)),
  Pval     = as.vector(sapply(y, "[[", 3)),
  Pattern  = as.vector(sapply(y, "[[", 7)),
  MC_Error = as.vector(sapply(y, "[[", 9))
)
yy