papiResults: An example of the data frame produced by 'papi'.

In PAPi: Predict metabolic pathway activity based on metabolomics data

Description

An example of the data frame produced by papi, where the first column contains the name of the metabolic pathways identified and the following columns contains their respective Activity Score (AS) in the different samples analyzed.

Usage

data(papiResults)

Format

A data frame where the first column contains the name of the metabolic pathways identified and the following columns contains their respective Activity Score (AS) in the different samples analyzed.

pathwayname

a list of metabolic pathways identified.

Sample1

the AS of each metabolic pathway in Sample 1

Sample2

the AS of each metabolic pathway in Sample 2

Sample3

the AS of each metabolic pathway in Sample 3

Sample4

the AS of each metabolic pathway in Sample 4

Sample5

the AS of each metabolic pathway in Sample 5

Sample6

the AS of each metabolic pathway in Sample 6

Examples

data(papiResults)
print(papiResults)

Example output

Loading required package: svDialogs
Loading required package: KEGGREST
                                     pathwayname          Sample1 Sample2
1                                     Replicates            cond1   cond1
22                                Bile secretion              140     105
10                            Methane metabolism               92     120
20                              ABC transporters             79.2    59.4
13      Pentose and glucuronate interconversions            63.25    82.5
12        Nicotinate and nicotinamide metabolism             56.4    70.5
6                 Glycerophospholipid metabolism             55.2      69
21   Amino sugar and nucleotide sugar metabolism            53.35    38.8
8                  Inositol phosphate metabolism             48.3      63
17               Terpenoid backbone biosynthesis             46.2      63
4                           Galactose metabolism 42.3666666666667    49.2
3                Fructose and mannose metabolism             41.6    51.2
5                        Glycerolipid metabolism             39.6    49.5
14                           Pyruvate metabolism             38.4      48
26                  Indole alkaloid biosynthesis             37.6    28.2
30               Phosphotransferase system (PTS)             36.8    27.6
19                         Vitamin B6 metabolism             35.2      48
33                          Two-component system               32      24
18                           Thiamine metabolism             28.6      39
31                 Starch and sucrose metabolism            28.05    20.4
2    Carbon fixation in photosynthetic organisms            26.45    34.5
7                   Glycolysis / Gluconeogenesis            26.35   29.45
16                     Pentose phosphate pathway             24.2    25.3
23           Butirosin and neomycin biosynthesis             23.2    17.4
29                            Mineral absorption             23.2    17.4
24         Carbohydrate digestion and absorption             21.6    16.2
32                     Streptomycin biosynthesis             19.2    14.4
25                       HIF-1 signaling pathway               12       9
15                  Clavulanic acid biosynthesis               11      15
34                     Type II diabetes mellitus              4.8     3.6
110        Biosynthesis of secondary metabolites              3.4     3.8
9                             Metabolic pathways              3.4     3.8
27                     Insulin signaling pathway              3.2     2.4
11  Microbial metabolism in diverse environments              2.6     3.2
28                               Meiosis - yeast              2.4     1.8
             Sample3          Sample4 Sample5 Sample6
1              cond1            cond2   cond2   cond2
22             122.5              210   192.5   262.5
10               100               16      24      16
20              69.3            118.8   108.9   148.5
13             68.75               11    16.5      11
12              61.1              9.4    14.1     9.4
6               59.8              9.2    13.8     9.2
21             53.35             87.3    87.3   106.7
8               52.5              8.4    12.6     8.4
17              50.4             <NA>    <NA>    <NA>
4   43.7333333333333             28.7    28.7   34.85
3               46.4             19.2      24    21.6
5               42.9              6.6     9.9     6.6
14              41.6              6.4     9.6     6.4
26              32.9             56.4    51.7    70.5
30              32.2             55.2    50.6      69
19              38.4             <NA>    <NA>    <NA>
33                28               48      44      60
18              31.2             <NA>    <NA>    <NA>
31             28.05             45.9    45.9    56.1
2              28.75              4.6     6.9     4.6
7               27.9 20.6666666666667    21.7    24.8
16              25.3             29.7    29.7    36.3
23              20.3             34.8    31.9    43.5
29              20.3             34.8    31.9    43.5
24              18.9             32.4    29.7    40.5
32              16.8             28.8    26.4      36
25              10.5               18    16.5    22.5
15                12             <NA>    <NA>    <NA>
34               4.2              7.2     6.6       9
110              3.6                2     2.1     2.4
9                3.6                2     2.1     2.4
27               2.8              4.8     4.4       6
11               2.9              0.8       1     0.9
28               2.1              3.6     3.3     4.5

PAPi documentation built on Oct. 31, 2019, 3:19 a.m.