Introduction:
This tool inputs a peak table file and performs intra
correlation analysis on the metabolites.
Input files:
1.
Peak table file in Tab-delimited
txt format, first column is the compound identifier, the others are samples.
For example:
|
HU_011 |
HU_014 |
HU_015 |
HU_017 |
HU_018 |
HU_019 |
|
|
(2-methoxyethoxy)propanoic acid isomer |
3.019766 |
3.814339 |
3.519691 |
2.562183 |
3.781922 |
4.161074 |
|
(gamma)Glu-Leu/Ile |
3.888479 |
4.277149 |
4.195649 |
4.32376 |
4.629329 |
4.412266 |
|
1-Methyluric acid |
3.869006 |
3.837704 |
4.102254 |
4.53852 |
4.178829 |
4.516805 |
|
1-Methylxanthine |
3.717259 |
3.776851 |
4.291665 |
4.432216 |
4.11736 |
4.562052 |
|
1,3-Dimethyluric acid |
3.535461 |
3.932581 |
3.955376 |
4.228491 |
4.005545 |
4.320582 |
|
1,7-Dimethyluric acid |
3.325199 |
4.025125 |
3.972904 |
4.109927 |
4.024092 |
4.326856 |
|
2-acetamido-4-methylphenyl acetate |
4.204754 |
5.181858 |
3.88568 |
4.237915 |
1.852994 |
4.080681 |
|
2-Aminoadipic acid |
4.080204 |
4.359246 |
4.249111 |
4.231404 |
4.323679 |
4.244485 |
Parameter:
Correlation methods:
1.
Kendall rank correlation:
The Kendall rank correlation coefficient,
commonly referred to as Kendall's tau coefficient (after the Greek letter τ),
is a statistic used to measure the ordinal association between two measured
quantities. A tau test is a non-parametric hypothesis test for statistical
dependence based on the tau coefficient.
2.
Pearson correlation:
the Pearson correlation coefficient, also
referred to as Pearson's r is a measure of the linear correlation between two
variables X and Y. It has a value between +1 and −1, where 1 is total positive
linear correlation, 0 is no linear correlation, and −1 is total negative linear
correlation.
3.
Spearman correlation:
Spearman's rank correlation coefficient or
Spearman's rho is a nonparametric measure of rank correlation. It assesses how
well the relationship between two variables can be described using a monotonic
function.
Output files:
1.
'Intra_r_Matrix.txt', the matrix
of correlations.
2.
'Intra_Correlation_Heatmap.pdf',
correlation heatmap plot.
3.
'Intra_P_Matrix.txt', the matrix
of P-values.
4.
'Intra_Corrected_P_Matrix.txt', the
matrix of Corrected P-values.
5.
'Network_Edges_for_Cytoscape.txt',
network edges information for Cytoscape software.
6.
'Network_Nodes_for_Cytoscape.txt',
network nodes information for Cytoscape software.