getStatistics | R Documentation |
Extract the list of p-values or/and log fold changes from the output of a differential abundance detection method.
getStatistics( method, slot = "pValMat", colName = "rawP", type = "pvalue", direction = NULL, verbose = FALSE )
method |
Output of a differential abundance detection method.
|
slot |
The slot name where to extract values
(default |
colName |
The column name of the slot where to extract values
(default |
type |
The value type of the column selected where to extract values.
Two values are possible: |
direction |
|
verbose |
Boolean to display the kind of extracted values
(default |
A vector or a data.frame
. If direction = NULL
,
the colname
column values, transformed according to type
(not
tranformed if type = "pvalue"
, -abs(value)
if
type = "logfc"
), of the slot
are reported, otherwise the
direction
column of the statInfo
matrix is added to the output.
extractStatistics
data("ps_plaque_16S") # Add scaling factors ps_plaque_16S <- norm_edgeR(object = ps_plaque_16S, method = "TMM") # DA analysis da.limma <- DA_limma( object = ps_plaque_16S, design = ~ 1 + HMP_BODY_SUBSITE, coef = 2, norm = "TMM" ) # get p-values getStatistics( method = da.limma, slot = "pValMat", colName = "rawP", type = "pvalue", direction = NULL ) # get negative abs(logFC) values getStatistics( method = da.limma, slot = "statInfo", colName = "logFC", type = "logfc", direction = NULL ) # get p-values and logFC getStatistics( method = da.limma, slot = "pValMat", colName = "rawP", type = "pvalue", direction = "logFC" )
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