CheckAssay.Rd
Check the classes, dimensions, missingness, feature variance, feature type, and feature names of a data frame.
CheckAssay(df, removeNear0 = TRUE, epsilon = 10^-6)
df | An assay data frame supplied to the |
---|---|
removeNear0 | Should columns of |
epsilon | Threshold to consider the variance of a column equal to 0. Defaults to 0.000001. |
The same data frame, without features with 0 variance, if that data frame passes all checks.
This function checks that the data frame is not a matrix, that the
data frame has more columns than rows (tidy genomic data), that the data
frame contains no missing or character values, that no features of the
data frame have variance less than epsilon
(and removes such
features if removeNear0 = TRUE
), and checks the data frame for
valid column names.
# DO NOT CALL THIS FUNCTION DIRECTLY. CALL FROM WITHIN CreateOmics(). if (FALSE) { data("colonSurv_df") CheckAssay(colonSurv_df[, -(1:3)]) }