baseline_exprs {dtangle} | R Documentation |
Estimate the offset terms.
baseline_exprs(Y, pure_samples, markers, summary_fn = mean)
Y |
Expression matrix. (Required) Two-dimensional numeric. Must implement Each row contains expression measurements for a particular sample. Each columm contains the measurements of the same gene over all individuals. Can either contain just the mixture samples to be deconvolved or both the mixture samples and the reference samples. See |
pure_samples |
The pure sample indicies. (Optional) List of one-dimensional integer. Must implement The i-th element of the top-level list is a vector of indicies (rows of |
markers |
Marker gene indices. (Optional) List of one-dimensional integer. Top-level list should be same length as |
summary_fn |
What summary statistic to use when aggregating expression measurements. (Optional) Function that takes a one-dimensional vector of numeric and returns a single numeric. Defaults to the mean. Other good options include the median. |
List of vectors. Each vector is estimated estimated basline in pure samples of markers for each group, resp.
truth = shen_orr_ex$annotation$mixture
pure_samples <- lapply(1:3, function(i) {
which(truth[, i] == 1)
})
Y <- shen_orr_ex$data$log
markers = find_markers(Y=Y,
pure_samples = pure_samples,data_type='microarray-gene',marker_method='ratio')$L
K = length(pure_samples)
n_markers = rep(20,K)
mrkrs <- lapply(1:K, function(i) {
markers[[i]][1:n_markers[i]]
})
dtangle:::baseline_exprs(Y, pure_samples, mrkrs)