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What the Package Does (One Line, Title Case)

License: Other

R 100.00%

request's Introduction

request

The goal of request is to ...

Installation

You can install the released version of request from CRAN with:

install.packages("request")

Example

This is a basic example which shows you how to solve a common problem:

library(request)
## basic example code

sampleList$sampleID
sampleList$samplePositionInBox
sampleList$boxID

requestList <- makeRL(sampleList, "method")

  slots <- getSampleSlots(numberOfSamples, "method")
  slots$plateNumber
  slots$slotPosition

  newPositions <- getPositions(sampleList, slots)
  newPositions$samplePositionOnPlate
  
requestList$sampleID
requestList$samplePositionInBox
requestList$boxID
requestList$samplePositionOnPlate
requestList$plateNumber

runOrder <- makeRO(requestList, "method")


method@availableSlots = list()
method@methodSpecificSamples = list(sample, position)

request's People

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siobhon-egan

request's Issues

fix display for layout

currently missing samples are not displayed properly and only shift the table entries

Change to data paths on IVDR03 and IVDR02 experiments

Due to computer updates, the directory where data is stored has now changed for IVDR02 and IVDR03.

Please change dev_path for IVDR02 and IVDR03 from C:\IVDrData\data to D:\IVDrData\data

https://docs.google.com/spreadsheets/d/e/2PACX-1vQs_oa0dMN6RE837QQ6GgQHFQr85SnjJZExxBarrWhEClCqHWEjEEp_bhtNwpbAlWpucbda9RhrkWTp/pub?gid=1146951709&single=true&output=tsv

create run order for eicosanoids

MS_Eicosanoids_BARWINp01_request_EXAMPLE.csv

use this file as an example

Fix concentration for MS-AA assay

update bile acid methods

Request from @sungchin to update MS bile acid methods.
Can you please amend L180-L182 in classRequestList.R to the following:

            msFile <- "BileAcids_MS_2022"
            msTunFile <- "BileAcids_Tune_2022"
            inletFile <- "BileAcids_LC_2022"

add function to assign plateID for paired samples

look at function in makeConfigFiles.Rmd in heidelberg cohort line 124

NMR holder number

Issue with revised NMR run order generation.
The "HOLDER" is not formatting correctly and is giving a new position for each experiment even though sample is the same.

Not sure if it is getting this information from getrun.r.

Issues noticed by Philipp from diabetes/exercise run orders.

run the Calibration and QC in increasing order from CAL-01 to CAL-08

this means that concentration must be inverted so that the lowest concentration are run first (lowest concentration are also located at the top of the plate, from A to H)

make sure LTR or QC are run every 10 samples

New matrixID

Can I please request new addition to sample type to matrixID

Can we please add the following:

10 BALF Bronchoalveolar lavage fluid

https://docs.google.com/spreadsheets/d/e/2PACX-1vQs_oa0dMN6RE837QQ6GgQHFQr85SnjJZExxBarrWhEClCqHWEjEEp_bhtNwpbAlWpucbda9RhrkWTp/pub?gid=481322438&single=true&output=tsv

take column headers from TRY (waters) and use them for BILE (as suggested by Luke)

TRY headers are imported correctly in other softwares

check NMR run oder

check how columnwise run order would affect the numbering of the experiments (expno) if not then turn nmr columnwise

add extension as per method basis

currently all configuration files share the same tsv. But some as Try should end with a .txt extension

add proper LTR per method basis

currently we use plasma LTR for all methods

make naming of Calibration and QC samples coherent for all methods

The new names should be CAL-01 and QC-01 for all methods (when possible) AA, TRY, LIPIDS, EICOS, and BILE

findAllEmptyPositions

Getting an error for the function findAllEmptyPositions

for (s in which(is.na(selectedSamples$wellPos))){
  pos <- findAllEmptyPositions(selectedSamples, boxDim = c(8, 10), by = "col")$position[1]
  RC <- posToRC(pos, collapse = TRUE)
  selectedSamples$wellPos[s] <- pos
  selectedSamples$wellRC[s] <- RC
}

Output

Error in findAllEmptyPositions(selectedSamples, boxDim = c(8, 10), by = "col") : 
  could not find function "findAllEmptyPositions"

It works when I manually import function into R however does not recognise it when I load the request package.

altler lipid run orders

leave LTR in column 12 and and use column 11 for pqc (all without ids)