QC: Count data quality check

In NBBttest: Negative Binomial Beta t-Test

Count data quality check

Description

QC is used to check quality of count data in two ways: scatter plot of two replicated samples and correlation heatmap of all samples.

Usage

QC(dat, nci, S1="NULL", S2="NULL", method=
"plot", colrs="greenred", rwcex=1.8, clcex=1.8, 
x=10, tree="none", log="none", col="blue", 
pch=19, labsize=1.5, axis=1.5)

Arguments

dat	count matric dataset.
nci	number of columns containing data information suach as gene id, library id, target id, gene name, strand etc.
S1	numeric int value, indicating which column in data matrix is specified in x-axis. S1 > nci.
S2	numeric int value, indicating which column in data matrix is specified in y-axis. S2> nci.
method	string. Here two methods are given for choice: "plot" and "heatmap". Default is "plot".
colrs	string. 8 color sets are given for choice in this function: "redgreen", "heat.colors", "redblue", "greenred", "bluered", "cm.colors", "terrain.colors", "topo.colors". The default color set is "redgreen".
rwcex	positive numbers, used as cex.axis for the row axis labeling. The default value is 1.8.
clcex	positive numbers, used as cex.axis for the column axis labeling. The default value is 1.8.
x	numeric argument: positive number, used as argument of cm.colors(x), terrain.colors(x) and topo.colors(x), the default value is 10.
tree	tree(s) drwan on row or column or both. User has four options: "both" for drawing trees on both row and column,"row" for drawing treeonly on row,"column" for drawing tree on only column, and "none" for no tree specified. Default is "none".
log	string. Two options are given for choice: "none" and "log". log="log" indicates that data value would be transfomed with log2. Default is "none".
col	string, used to specify scatter plot dot color.
pch	numeric value, used to specify dot type.
labsize	numeric value for size of xlabel and ylabel
axis	numeric value for axis scale.

Details

S1, S2 and nci must be given numeric int values for plot and heatmap. However, when method is chosen to be "heatmap", then S1 and S2 are not specified. Columns of information should be left of matrix and count data should be after columns of information.

Value

not return values but create scatter plot or heatmap plot.

Note

requires gplots and grDevices.

Author(s)

Yuan-De Tan [e-mail]

See Also

heatmap.2 and grDevices

Examples

data(jkttcell)
QC(dat=jkttcell, nci=7, S1=8, S2=9, method = "plot", 
log = "log", col = "blue", pch = 19)
QC(dat=jkttcell, nci=7, S1=8, S2=9, method = "plot", 
log = "log", col = "blue", pch = 19)
QC(dat=jkttcell, nci=7, method = "heatmap", log = "log")

NBBttest documentation built on May 30, 2022, 1:05 a.m.