Description Usage Arguments Details Value Author(s) See Also Examples
Function visualises time dependent behaviour of genes in two compared groups. The natural cubic spline regression curves fitted to discrete, time dependent expression data are plotted. One plot shows two curves  representing the reference group and the compared group, respectively. See also splineDiffExprs
function.
1  splinePlot(eSetObject, df, reference, toPlot="all")

eSetObject 

df 
number of degrees of freedom 
reference 
character defining which treatment group should be considered as reference 
toPlot 
vector of genes to plot; defalut is 
The input eSetObject
must be provided as an object of class ExpressionSet
which contains SampleName
, Time
, Treatment
and if applicable Replicates
variables (columns) included in the phenotypic data of the eSetObject
(pData(eSetObject)
). Two types of Treatment
defining two groups to compare have to be definied.
Replicates are not required. The time points for compared treatment groups should be identical.
User has to define number of degrees of freedom (df
) for the spline regression model. Choosing effective degrees of freedom in range 35 is reasonable.
Genes to plot, given as a vector of characters, can be selected by the user. Provided names have to be a part of a row name vector of eSetObject
(rownames(exprs(eSetObject))
). If genes to plot are not definied, all genes are plotted.
A .pdf file containing plots for chosen genes.
Agata Michna
1 2 3 4 5 6 7 8 9 10 
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SampleName Time Treatment Replicate
1 T1_1_A 1 T1 A
2 T1_4_A 4 T1 A
3 T1_8_A 8 T1 A
4 T1_16_A 16 T1 A
5 T1_24_A 24 T1 A
6 T1_32_A 32 T1 A
7 T1_40_A 40 T1 A
8 T1_48_A 48 T1 A
9 T1_1_B 1 T1 B
10 T1_4_B 4 T1 B
11 T1_8_B 8 T1 B
12 T1_16_B 16 T1 B
13 T1_24_B 24 T1 B
14 T1_32_B 32 T1 B
15 T1_40_B 40 T1 B
16 T1_48_B 48 T1 B
17 T2_1_A 1 T2 A
18 T2_4_A 4 T2 A
19 T2_8_A 8 T2 A
20 T2_16_A 16 T2 A
21 T2_24_A 24 T2 A
22 T2_32_A 32 T2 A
23 T2_40_A 40 T2 A
24 T2_48_A 48 T2 A
25 T2_1_B 1 T2 B
26 T2_4_B 4 T2 B
27 T2_8_B 8 T2 B
28 T2_16_B 16 T2 B
29 T2_24_B 24 T2 B
30 T2_32_B 32 T2 B
31 T2_40_B 40 T2 B
32 T2_48_B 48 T2 B
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