groupGenerics: Group Generics for 'soma_adat' Class Objects

In SomaDataIO: Input/Output 'SomaScan' Data

Group Generics for soma_adat Class Objects

Description

S3 group generic methods to apply group specific prototype functions to the RFU data only of soma_adat objects. The clinical meta data are not transformed and remain unmodified in the returned object (Math() and Ops()) or are ignored for the Summary() group. See groupGeneric().

Usage

## S3 method for class 'soma_adat'
Math(x, ...)

antilog(x, base = 10)

## S3 method for class 'soma_adat'
Ops(e1, e2 = NULL)

## S3 method for class 'soma_adat'
Summary(..., na.rm = FALSE)

## S3 method for class 'soma_adat'
e1 == e2

Arguments

x	The soma_adat class object to perform the transformation.
...	Additional arguments passed to the various group generics as appropriate.
base	A positive or complex number: the base with respect to which logarithms are computed.
e1, e2	Objects.
na.rm	Logical. Should missing values be removed?

Value

A soma_adat object with the same dimensions of the input object with the feature columns transformed by the specified generic.

Functions

• antilog(): performs the inverse or anti-log transform for a numeric vector of soma_adat object. note: default is base = 10, which differs from the log() default base e.

• Ops(soma_adat): performs binary mathematical operations on class soma_adat. See Ops().

• Summary(soma_adat): performs summary calculations on class soma_adat. See Summary().

• == : compares left- and right-hand sides of the operator unless the RHS is also a soma_adat, in which case diffAdats() is invoked.

Math

Group members:

#>  [1] "abs"      "acos"     "acosh"    "asin"     "asinh"    "atan"    
#>  [7] "atanh"    "ceiling"  "cos"      "cosh"     "cospi"    "cummax"  
#> [13] "cummin"   "cumprod"  "cumsum"   "digamma"  "exp"      "expm1"   
#> [19] "floor"    "gamma"    "lgamma"   "log"      "log10"    "log1p"   
#> [25] "log2"     "sign"     "sin"      "sinh"     "sinpi"    "sqrt"    
#> [31] "tan"      "tanh"     "tanpi"    "trigamma" "trunc"

Commonly used generics of this group include:

• log(), log10(), log2(), antilog(), abs(), sign(), floor(), sqrt(), exp()

Ops

Group members:

#>  [1] "+"   "-"   "*"   "^"   "%%"  "%/%" "/"   "=="  ">"   "<"   "!="  "<=" 
#> [13] ">="

Note that for the ⁠`==`⁠ method if the RHS is also a soma_adat, diffAdats() is invoked which compares LHS vs. RHS. Commonly used generics of this group include:

• +, -, *, /, ^, ==, >, <

Summary

Group members:

#> [1] "all"   "any"   "max"   "min"   "prod"  "range" "sum"

Commonly used generics of this group include:

• max(), min(), range(), sum(), any()

Author(s)

Stu Field

See Also

groupGeneric(), getGroupMembers(), getGroup()

Examples

# subset `example_data` for speed
# all SeqIds from 2000 -> 2999
seqs <- grep("^seq\\.2[0-9]{3}", names(example_data), value = TRUE)
ex_data_small <- head(example_data[, c(getMeta(example_data), seqs)], 10L)
dim(ex_data_small)

ex_data_small$seq.2991.9

# Math Generics:
# -------------
# log-transformation
a <- log(ex_data_small)
a$seq.2991.9

b <- log10(ex_data_small)
b$seq.2991.9
isTRUE(all.equal(b, log(ex_data_small, base = 10)))

# floor
c <- floor(ex_data_small)
c$seq.2991.9

# square-root
d <- sqrt(ex_data_small)
d$seq.2991.9

# rounding
e <- round(ex_data_small)
e$seq.2991.9

# inverse log
antilog(1:4)

alog <- antilog(b)
all.equal(ex_data_small, alog)    # return `b` -> linear space

# Ops Generics:
# -------------
plus1 <- ex_data_small + 1
times2 <- ex_data_small * 2

sq <- ex_data_small^2
all.equal(sqrt(sq), ex_data_small)

gt100k <- ex_data_small > 100000
gt100k

ex_data_small == ex_data_small   # invokes diffAdats()

# Summary Generics:
# -------------
sum(ex_data_small)

any(ex_data_small < 100)  # low RFU analytes

sum(ex_data_small < 100)  # how many

min(ex_data_small)

min(ex_data_small, 0)

max(ex_data_small)

max(ex_data_small, 1e+7)

range(ex_data_small)

SomaDataIO documentation built on April 4, 2025, 2:14 a.m.