QC: Count data quality check

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/QC.R

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

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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 tanyuande@gmail.com

See Also

heatmap.2 and grDevices

Examples

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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 July 2, 2020, 3:37 a.m.