Description Usage Arguments Value See Also Examples
This help file describes different ways to access the slots and values contained in uwmwRes
objects resulting from calls to uWMW
, and in uwmwEstimate
objects resulting from calls to getEstimate
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 | type(x)
## S4 method for signature 'uwmwRes'
type(x)
## S4 method for signature 'uwmwEstimate'
type(x)
## S4 method for signature 'uwmwRes'
housekeeping(x)
## S4 method for signature 'uwmwEstimate'
housekeeping(x)
## S4 method for signature 'uwmwRes'
names(x)
## S4 method for signature 'uwmwEstimate'
names(x)
## S4 method for signature 'uwmwRes'
logor(x, ordered = TRUE)
## S4 method for signature 'uwmwRes'
se(x, ordered = TRUE)
## S4 method for signature 'uwmwEstimate'
se(x)
## S4 method for signature 'uwmwRes'
oddsRatio(x, ordered = TRUE)
## S4 method for signature 'uwmwRes'
zval(x, ordered = TRUE)
## S4 method for signature 'uwmwRes'
pval(x, ordered = TRUE)
## S4 method for signature 'uwmwRes'
coef(object)
## S4 method for signature 'uwmwRes'
vcov(object)
## S4 method for signature 'uwmwEstimate'
ref(x)
## S4 method for signature 'uwmwEstimate'
esttype(x)
## S4 method for signature 'uwmwRes'
getOrder(x)
is.unsorted(x, na.rm = FALSE, strictly = FALSE)
## S4 method for signature 'uwmwRes'
orderedBy(x)
## S4 method for signature 'uwmwEstimate'
orderedBy(x)
## S4 method for signature 'uwmwRes'
groupinfo(x)
## S4 method for signature 'uwmwEstimate'
groupinfo(x)
## S4 method for signature 'uwmwEstimate'
length(x)
## S4 method for signature 'uwmwRes'
length(x)
|
x |
a uwmwRes object or a uwmwEstimate object. |
ordered |
logical value. If set to |
object |
see |
na.rm |
for compatibility with the base function |
strictly |
for compatibility with the base function |
type(x)
returns the type of uWMW carried out (i.e. O or H for using overall respectively housekeeping expression as a reference.)
housekeeping(x)
returns the content of the housekeeping slot from the object. Or, in case of overall normalization, it returns NULL.
names(x)
returns the names of the genes in the object, and in the order defined in the object.
logor(x)
returns a numeric vector with the log OR values.
se(x)
returns a numeric vector with the standard errors on the logor.
oddsRatio(x)
returns a numeric vector with the odds ratios.
zval(x)
returns a numerical vector with the Z values contained in the object.
pval(x)
returns a numerical vector containing the p values in the object.
orderedBy(x)
returns the slot by which the object is ordered (i.e. the value of the slot orderedBy)
groupinfo(x)
returns the groupinfo slot, i.e. a character vector of length 2 that indicates in which order the groups are compared by uWMW.
uwmw_Extract
for matrix like extraction of data.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | data(NBmat)
NBtest <- uWMW(NBmat,NBgroups)
coef(NBtest)[1:10]
type(NBtest)
# With a sorted object
NBsort <- sort(NBtest, which="p")
is.unsorted(NBtest)
is.unsorted(NBsort)
orderedBy(NBsort)
# On an Estimate object
NBlogodds <- getEstimate(NBsort,"logodds")
se(NBlogodds)
# and so on...
|
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