Description Usage Arguments Value See Also Examples
This function extracts Wald test results from a sleuth object.
1 2 | sleuth_results(obj, test, test_type = "wt", which_model = "full",
rename_cols = TRUE, show_all = TRUE)
|
obj |
a |
test |
a character string denoting the test to extract. Possible tests can be found by using |
which_model |
a character string denoting the model. If extracting a wald test, use the model name. If extracting a likelihood ratio test, use 'lrt'. |
rename_cols |
if |
show_all |
if |
a data.frame
with the following columns:
target_id: transcript name, e.g. "ENSXX#####" (dependent on the transcriptome used in kallisto)
pval: p-value of the chosen model
qval: false discovery rate adjusted p-value, using Benjamini-Hochberg (see p.adjust
)
b: 'beta' value (effect size). Technically a biased estimator of the fold change
se_b: standard error of the beta
mean_obs: mean of natural log counts of observations
var_obs: variance of observation
tech_var: technical variance of observation from the bootstraps
sigma_sq: raw estimator of the variance once the technical variance has been removed
smooth_sigma_sq: smooth regression fit for the shrinkage estimation
final_simga_sq: max(sigma_sq, smooth_sigma_sq); used for covariance estimation of beta
sleuth_wt
and sleuth_lrt
to compute tests, models
to
view which models, tests
to view which tests were performed (and can be extracted)
1 2 3 | models(sleuth_obj) # for this example, assume the formula is ~condition,
and a coefficient is IP
results_table <- sleuth_results(sleuth_obj, 'conditionIP')
|
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