{"action":"created","issue":{"url":"https://api.github.com/repos/lgatto/synapter/issues/39","repository_url":"https://api.github.com/repos/lgatto/synapter","labels_url":"https://api.github.com/repos/lgatto/synapter/issues/39/labels{/name}","comments_url":"https://api.github.com/repos/lgatto/synapter/issues/39/comments","events_url":"https://api.github.com/repos/lgatto/synapter/issues/39/events","html_url":"https://github.com/lgatto/synapter/issues/39","id":10171526,"number":39,"title":"Correct saturation by only quantifying on unsaturated isotopes in all samples under comparison","user":{"login":"pavel-shliaha","id":1895805,"avatar_url":"https://avatars.githubusercontent.com/u/1895805?v=3","gravatar_id":"","url":"https://api.github.com/users/pavel-shliaha","html_url":"https://github.com/pavel-shliaha","followers_url":"https://api.github.com/users/pavel-shliaha/followers","following_url":"https://api.github.com/users/pavel-shliaha/following{/other_user}","gists_url":"https://api.github.com/users/pavel-shliaha/gists{/gist_id}","starred_url":"https://api.github.com/users/pavel-shliaha/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pavel-shliaha/subscriptions","organizations_url":"https://api.github.com/users/pavel-shliaha/orgs","repos_url":"https://api.github.com/users/pavel-shliaha/repos","events_url":"https://api.github.com/users/pavel-shliaha/events{/privacy}","received_events_url":"https://api.github.com/users/pavel-shliaha/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/lgatto/synapter/labels/enhancement","name":"enhancement","color":"84b6eb"},{"url":"https://api.github.com/repos/lgatto/synapter/labels/in%20progress","name":"in progress","color":"ededed"}],"state":"open","locked":false,"assignee":{"login":"sgibb","id":1828443,"avatar_url":"https://avatars.githubusercontent.com/u/1828443?v=3","gravatar_id":"","url":"https://api.github.com/users/sgibb","html_url":"https://github.com/sgibb","followers_url":"https://api.github.com/users/sgibb/followers","following_url":"https://api.github.com/users/sgibb/following{/other_user}","gists_url":"https://api.github.com/users/sgibb/gists{/gist_id}","starred_url":"https://api.github.com/users/sgibb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sgibb/subscriptions","organizations_url":"https://api.github.com/users/sgibb/orgs","repos_url":"https://api.github.com/users/sgibb/repos","events_url":"https://api.github.com/users/sgibb/events{/privacy}","received_events_url":"https://api.github.com/users/sgibb/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/lgatto/synapter/milestones/1","html_url":"https://github.com/lgatto/synapter/milestones/2.0","labels_url":"https://api.github.com/repos/lgatto/synapter/milestones/1/labels","id":849290,"number":1,"title":"2.0","description":"","creator":{"login":"sgibb","id":1828443,"avatar_url":"https://avatars.githubusercontent.com/u/1828443?v=3","gravatar_id":"","url":"https://api.github.com/users/sgibb","html_url":"https://github.com/sgibb","followers_url":"https://api.github.com/users/sgibb/followers","following_url":"https://api.github.com/users/sgibb/following{/other_user}","gists_url":"https://api.github.com/users/sgibb/gists{/gist_id}","starred_url":"https://api.github.com/users/sgibb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sgibb/subscriptions","organizations_url":"https://api.github.com/users/sgibb/orgs","repos_url":"https://api.github.com/users/sgibb/repos","events_url":"https://api.github.com/users/sgibb/events{/privacy}","received_events_url":"https://api.github.com/users/sgibb/received_events","type":"User","site_admin":false},"open_issues":11,"closed_issues":32,"state":"open","created_at":"2014-11-01T11:05:40Z","updated_at":"2016-04-11T20:46:47Z","due_on":null,"closed_at":null},"comments":56,"created_at":"2013-01-21T21:04:32Z","updated_at":"2016-05-19T16:51:22Z","closed_at":null,"body":"The prototype of suggested function:\r\n\r\nrequantify <- function (synapterObj ,  satThreshold, minIsotopes)\r\n\r\nsynapterObj  - list of synapter objects\r\nsatThreshold - intensity over which accurate ion recording is not possible, due to saturation\r\nminIsotopes  - minimum number of isotopes accepted for requantitation\r\n\r\nFor every peptide the function will find common unsaturated ions from supplied synapter objects, and requqntify EMRT using these ions only. satThreshold  is used to determine which ions saturate. minIsotopes is the minimum number of isotopes that are sufficient to requantify (i.e. sometimes only few isotopes will be seen in all samples under saturation and over LOD)\r\n\r\nImportant: the information on peptide isotopes is not presented in current synapter objects! Pep3D file that is loaded in synapter is filtered so that for each EMRT only one isotope is preserved. This means that synapter object will have to be modified to include this information. Current consensus is that a list should be created each element of which represents a single EMRT and contains information on ion intensities from those EMRTs\r\n"},"comment":{"url":"https://api.github.com/repos/lgatto/synapter/issues/comments/220385196","html_url":"https://github.com/lgatto/synapter/issues/39#issuecomment-220385196","issue_url":"https://api.github.com/repos/lgatto/synapter/issues/39","id":220385196,"user":{"login":"pavel-shliaha","id":1895805,"avatar_url":"https://avatars.githubusercontent.com/u/1895805?v=3","gravatar_id":"","url":"https://api.github.com/users/pavel-shliaha","html_url":"https://github.com/pavel-shliaha","followers_url":"https://api.github.com/users/pavel-shliaha/followers","following_url":"https://api.github.com/users/pavel-shliaha/following{/other_user}","gists_url":"https://api.github.com/users/pavel-shliaha/gists{/gist_id}","starred_url":"https://api.github.com/users/pavel-shliaha/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pavel-shliaha/subscriptions","organizations_url":"https://api.github.com/users/pavel-shliaha/orgs","repos_url":"https://api.github.com/users/pavel-shliaha/repos","events_url":"https://api.github.com/users/pavel-shliaha/events{/privacy}","received_events_url":"https://api.github.com/users/pavel-shliaha/received_events","type":"User","site_admin":false},"created_at":"2016-05-19T16:51:22Z","updated_at":"2016-05-19T16:51:22Z","body":"Hey Sebastian,\r\n\r\nplease execute this code and tell me what you see\r\n\r\n\r\nlibrary(synapter)\r\n\r\ncombMSNSet <- readRDS (\"Y://RAW/pvs22//_QTOF_DATA_data3//synapter2paper//kuharev2015//synapter2//output//UDMSE//refcombMSNSet.RDS\")\r\nsatThresholdIon <- 3e4\r\n\r\nsatCorrected <- sapply (c (\"sat\", \"sum\", \"reference\"),\r\n                        function (x) NULL)\r\n\r\nsatCorrected[[1]] <- combMSNSet\r\n\r\nsatCorrected[[2]] <- requantify (combMSNSet, method = \"sum\", \r\n                                 saturationThreshold= satThresholdIon,\r\n                                 onlyCommonIsotopes=FALSE)\r\n\r\nsatCorrected[[3]]    <- requantify (combMSNSet, method = \"reference\", \r\n                                    saturationThreshold= satThresholdIon)\r\n\r\n# function to find requantified row\r\nfindDifferentquant <- function (MSnSet1, MSnSet2){\r\n  selA <- c () \r\n  for (i in 1:nrow (MSnSet1))  if (any (exprs(MSnSet1)[i, ] != exprs(MSnSet2)[i, ], na.rm = TRUE)) selA <- c (selA, i)\r\n  return (selA)\r\n}\r\n\r\ndiffSum <-  findDifferentquant(satCorrected[[1]], satCorrected[[2]])\r\ndiffRef <-  findDifferentquant(satCorrected[[1]], satCorrected[[3]])\r\n\r\nlength (diffSum)\r\nlength (diffRef)\r\n\r\nI see \r\n> length (diffSum)\r\n[1] 3069\r\n\r\nand\r\n\r\n> length (diffSum)\r\n[1] 3069\r\n\r\n> length (diffRef)\r\n[1] 3067\r\n\r\n"}}