jammacalc | R Documentation |
Calculate MA-plot data
jammacalc(
x,
na.rm = TRUE,
controlSamples = NULL,
centerGroups = NULL,
controlFloor = NA,
naControlAction = c("row", "floor", "min", "na"),
naControlFloor = 0,
groupedX = TRUE,
useMedian = TRUE,
useMean = NULL,
whichSamples = NULL,
noise_floor = -Inf,
noise_floor_value = noise_floor,
naValue = NA,
mad_row_min = 0,
grouped_mad = TRUE,
centerFunc = centerGeneData,
useRank = FALSE,
returnType = c("ma_list", "tidy"),
verbose = FALSE,
...
)
x |
|
na.rm |
|
controlSamples |
|
centerGroups |
|
groupedX |
|
useMedian |
|
useMean |
(deprecated) |
whichSamples |
|
noise_floor |
|
noise_floor_value |
single |
naValue |
single |
mad_row_min |
|
grouped_mad |
|
centerFunc |
|
returnType |
|
verbose |
|
... |
additional arguments are ignored. |
This function takes a numeric matrix as input, and calculates
data sufficient to produce MA-plots. The default output is a
list of two-column numeric matrices with "x"
and "y"
coordinates,
representing the group median and difference from median,
respectively.
The mean value can be used by setting useMedian=FALSE
.
Samples can be grouped using the argument centerGroups
.
In this case the y-axis value will be "difference from
group median."
Control samples can be specified for centering using the
argument controlSamples
. In this case, the y-axis value will
be "difference from control median".
The sample grouping, and control samples can be combined, in which case the y-axis values will be "difference from the control median within the centering group."
Other jam matrix functions:
centerGeneData()
,
jammanorm()
,
matrix_to_column_rank()
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.