Description Usage Arguments Value See Also Examples

View source: R/functions_cleane.R

Separates metabolites into groups based on pooled plasma missing rates so that different thresholds of metrics can be applied to each group.

1 | ```
subset_met(df, miss, numsplit = 5, mincut = 0.02, maxcut = 0.95)
``` |

`df` |
The metabolomics dataset, ideally read from the |

`miss` |
Vector of missing rates of equal length to number of rows in |

`numsplit` |
The number of equal sized sections to divide metabolites into based on missing rate of pooled plasma columns. Divides the range of missing rates between |

`mincut` |
A cutoff to specify that any metabolite with pooled plasma missing rate less than or equal to this value should be retained. Default is |

`maxcut` |
A cutoff to specify that any metabolite with pooled plasma missing rate greater than this values should be removed. Default is |

A list consisting of a number of elements equal to `numsplit`

. Each element contains a matrix of the given metabolite group based on the pooled plasma missing rate. The list keys are simple integers corresponding to the split number.

See `MetProc-package`

for examples of running the full process.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ```
library(MetProc)
#Read in metabolomics data
metdata <- read.met(system.file("extdata/sampledata.csv", package="MetProc"),
headrow=3, metidcol=1, fvalue=8, sep=",", ppkey="PPP", ippkey="BPP")
#Get indices of pooled plasma and samples
groups <- get_group(metdata,"PPP","X")
#Calculate a pooled plasma missing rate and sample missing rate
#for each metabolite in data
missrate <- get_missing(metdata,groups[['pp']],groups[['sid']])
#Group metabolites into 5 groups based on pooled plasma
#missing rate
subsets <- subset_met(metdata,missrate[['ppmiss']],5,.02,.95)
``` |

MetProc documentation built on May 29, 2017, 3:56 p.m.

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