Credential3.1

A bioinformatics tool for biologically-relavent feature extraction features and untargeted metabolomics method optimization.

Installation

devtools::install_github("pattilabwu/Credential3.1")
library(Credential3.1)

Input data format

The input data is a peaktable that contains at least 4 columns of data: "cc"-index No, "mz"- m/z value, "rt"- retention time and "i"-intensity This peaktable can be generated from XCMS or many other peak-picking algorithms. The name of the columns in the peaktable has to be "mz", "cc", "rt" and "i".


> features
      cc       mz       rt            i
 1: 4850 550.3067  851.529     5419.261
 2: 5013 558.3340  850.141     5854.929
 3: 4804 548.3008  850.391     5209.042
 4: 5029 560.3396  850.642     5998.703
 5: 4827 549.4886 1536.830 10604955.633
 6: 4852 550.4924 1536.830  4241038.103
 7: 4874 551.4955 1536.580  1206786.640
 8: 4896 552.4979 1536.590   139663.706
 9: 5282 580.5907 1536.580    28051.912
10: 5303 581.5949 1536.580   202953.667
11: 5315 582.5990 1536.580  1286416.952
12: 5324 583.6029 1536.330  5415255.371

Usage

credential = credentialing(peaktable1,peaktable2,ppm = 20,rtwin = 2,rtcom = 1, ratio1 = 1/1, ratio2 = 1/2, ratio_tol = 0.1, charges = 1:4)

For detailed illustration of the parameters, see:

help(credentialing)

data output

A list of tables will be generated and compiled in the 'credential' object shown above. It includes:

CredentialedFeatureR2F -- final round credentialed features from both peaktables

CredentialedFeatureR2 -- mz&rt matched features from both peaktables

CredentialedFeature1N2 -- features that fail to pass 2nd filtering from credentialed features #1

CredentialedFeature2N2 -- features that fail to pass 2nd filtering from credentialed features #2

CredentialedFeature1R1 -- first round credentialed features from peaktable #1

CredentialedFeature2R1 -- first round credentialed features from peaktable #2

knots1&knots2 -- possible isotope pairs from peaktable #1&#2

credentialedKnots1&credentialedKnots2 -- credentialed groups from isotope pairs table #1&#2

CredentialedFeatureGroups -- matched index between group #1&#2("quipu" is the index for credentialed groups)

Understanding the output data

#65 credentialed feature groups:

credential7$CredentialedFeatureR2F[quipu_1==65,]
   cc_1     mz_1     rt_1      int_1 knot_1 tail_1 quipu_1  ratio_1 cc_2     mz_2    rt_2      int_2 knot_2 tail_2 quipu_2  ratio_2 combined_ratio
1: 8843 833.6024 1594.130 123599.468   1090      0      65 8.961008 8854 833.6031 1593.79  77270.810    596      0     679 3.532957       2.536404
2: 8856 834.6063 1594.360  66766.104   1090      0      65 8.961008 8869 834.6067 1594.04  38324.387    596      0     679 3.532957       2.536404
3: 9336 872.7280 1593.995   6910.652   2180      0      65 8.961008 9333 872.7280 1593.79   7342.721   1578      0     679 3.532957       2.536404
4: 9346 873.7326 1594.360  29194.090   2180      0      65 8.961008 9344 873.7334 1593.54  40671.305   1578      0     679 3.532957       2.536404
5: 9354 874.7378 1593.880  96785.679   2180      0      65 8.961008 9353 874.7382 1593.54 131249.741   1578      0     679 3.532957       2.536404
6: 9364 875.7416 1594.110 192621.899   2180      0      65 8.961008 9365 875.7426 1593.54 230820.709   1578      0     679 3.532957       2.536404
7: 9372 876.7447 1593.860  13793.032   2180      1      65 8.961008 9377 876.7464 1593.21  21871.426   1578      1     679 3.532957       2.536404

cc_1/2: peak index number

mz_1/2: measured mz value

rt_1/2: retention time in seconds

int_1/2: intensity

knot_1/2: index for isotope pairs

tail_1/2: U13C peak or not

quipu_1/2: index for 1st round credentialed groups within each ratio condition

ratio_1/2: U12C/U13C ratio