| Type: | Package |
| Title: | Combine Data from Positive and Negative Ionization Mode Finding Common Entities |
| Version: | 1.4 |
| Date: | 2019-02-05 |
| Author: | Monica Calderon-Santiago |
| Maintainer: | Monica Calderon-Santiago <b42casam@uco.es> |
| Description: | Find common entities detected in both positive and negative ionization mode, delete this entity in the less sensible mode and combine both matrices. |
| License: | GPL-2 |
| Depends: | R(≥ 3.1.3), plyr |
| Suggests: | testthat |
| LazyData: | true |
| RoxygenNote: | 5.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2019-02-05 08:54:42 UTC; FQM227 |
| Repository: | CRAN |
| Date/Publication: | 2019-02-05 10:33:33 UTC |
Combine positive and negative matrices
Description
Take positive and negative matrices and combine them by deleting redundat entities.
Usage
CombinePolarities(POSITIVE, NEGATIVE, CommonEntitiesFiltered)
Arguments
POSITIVE |
A matrix with positive entities information (Compound Name, Mass, RT, and multiple columns with the area of the compound in samples) |
NEGATIVE |
A matrix with positive entities information (Compound Name, Mass, RT, and multiple columns with the area of the compound in samples) |
CommonEntitiesFiltered |
The data set generated with the FilterbyRT function. |
Examples
## Not run:
CombinePolarities(POSITIVE,NEGATIVE,CommonEntitiesFiltered)
## End(Not run)
Filter by RT residuals
Description
Remove those entities with residuals above and below a maximum and minimum specified value.
Usage
FilterbyRT(CommonEntitiesImproved, MaxResidual, MinResidual)
Arguments
CommonEntitiesImproved |
Data set resulted from the RemoveMismatch function |
MaxResidual |
Maximum residual allowed for RT+ vs RT- association |
MinResidual |
Minimum residual allowed for RT+ vs RT- association |
Value
Plot filtered (RT+ vs RT-, regression, "residuals vs predicted", and Q-Q plot)
New CommonEntities table filtered, obtained after removing entities with very high or low residuals or RT+ vs RT-.
Examples
## Not run:
CommonEntitiesFiltered<-FilterbyRT(CommonEntitiesImproved,MaxResidual=0.5,MinResidual=(-0.5))
## End(Not run)
Find entities presented in both polarities
Description
Takes matrices from positive and negative ionization mode and find entities in common.
Usage
FindCommon(POSITIVE, NEGATIVE, ADDUCTS, Masstolerance, RTtolerance)
Arguments
POSITIVE |
A matrix with positive entities information (Compound Name, Mass, RT, and multiple columns with the area of the compound in samples). |
NEGATIVE |
A matrix with positive entities information (Compound Name, Mass, RT, and multiple columns with the area of the compound in samples). |
ADDUCTS |
A matrix with positive adducts, negative adducts and their difference in mass. |
Masstolerance |
The tolerance in Da when considering the adducts that can be present in both matrices. |
RTtolerance |
The tolerance of retention time when comparing both polarities. It should be in the same units as the RT in POSITIVE and NEGATIVE matrices. |
Examples
## Not run:
CommonEntities<-FindCommon(POSITIVE,NEGATIVE,ADDUCTS,Masstolerance=0.02,RTtorelance=0.5)
## End(Not run)
Remove mismatched entities
Description
Remove those entities that have been associated to more than one adduct, retaining only the most probable.
Usage
RemoveMismatch(CommonEntities)
Arguments
CommonEntities |
(Matrix generated from the FindCommon function). |
Value
CommonEntitiesImproved The matrix without mismatched entities.
Examples
## Not run:
CommonEntitiesImproved<-RemoveMismatch(CommonEntities)
## End(Not run)
Study RT differences to lately remove outliers
Description
Study the correlation between RT in positive and negative ionization modes to find those entities that have been associated wrongly.
Usage
StudyRTdiff(CommonEntitiesImproved)
Arguments
CommonEntitiesImproved |
The resultant data set from the function RemoveMismatch |
Value
Plot (RT+ vs RT-, regression, "residuals vs predicted", and Q-Q plot)
The CommonEntitiesImproved dataset now included a new column with residuals of each entity for the RT+ vs RT- regression.
Examples
## Not run:
CommonEntitiesImproved<-StudyRTdiff(CommonEntitiesImproved)
## End(Not run)