The results of spicy()

spicy() returns a SpicyResults object: a list with the elements below. Use topPairs(), signifPlot(), spicyBoxPlot() and bind() on it, or take elements with $.

Details

Elements for the cell method (method = "cell", the default):

cellResults

the full table, one row per pair (and per level with more than two conditions): excess_ref, excess_comp, excess_difference, se, df, p_value, p_adj, tau2; with covariates or adjustAbundance = TRUE, what the test was adjusted for (adjusted_for), the effect and p-value of each adjustment (<covariate>_effect, <covariate>_p_value, abundance_effect) and the unadjusted test (unadjusted_difference, unadjusted_se, unadjusted_df, unadjusted_p_value, unadjusted_p_adj). For survival: score_coefficient, p_value, p_adj, hazard_ratio_sd, hr_p_value and, with adjustAbundance = TRUE, the p-value and hazard ratio without it. With several radii: r, the radius with the strongest evidence, and p_value_best_radius.

radiusResults

with several radii, the table at every radius.

pairwiseAssoc

a list with, for every pair, the effect in every image (NA where the pair could not be measured).

effect

"allocation" (the extra fraction of to cells with a from cell within r), "count" (the extra from cells within r of each to cell), or "kontextual" (Statial's Kontextual test).

imageWeights

a list with, for every pair, each image's weight in the test: its share of its condition's information (sums to 1 within each condition).

coefficient, p.value, se, statistic, df

matrices with one row per pair, as for the image method: the reference excess and the differences, and their tests.

condition, imageID, subject, nCells, r, k

the condition and patient of every image, the cell counts, and the settings of the analysis.

For the image method (method = "image") the object holds the matrices coefficient, p.value, se, statistic and df, and pairwiseAssoc, as in spicyR 1.x.

See also

spicy, topPairs, bind