FR: SAM (Significance Analysis of Microarrays) #237
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Change of QValues and significant Gene Count, added standard permutation scheme getPermutations
implemented new cut function and monotonized delta
changes in naming (e.g. bioitem replacing gene)
Add unit tests
bvenn
approved these changes
Nov 10, 2022
bvenn
requested changes
Nov 10, 2022
docs/Testing.fsx
Outdated
Comment on lines
999
to
1001
| let data1 = Array.map2 tupel rowheader preData1 | ||
| let data2 = Array.map2 tupel rowheader preData2 |
There was a problem hiding this comment.
replace with
let data1 = Array.zip rowheader preData1
let data2 = Array.zip rowheader preData2
docs/Testing.fsx
Outdated
| @@ -834,7 +842,7 @@ aErrorAcc | |||
| (***hide***) | |||
| aErrorAcc |> GenericChart.toChartHTML | |||
| (***include-it-raw***) | |||
|
|
|||
| aErrorAcc|> Chart.show | |||
|
ping |
|
Additionally, add a fold change field in the SAM type. |
bvenn
reviewed
Dec 6, 2022
docs/Testing.fsx
Outdated
Comment on lines
1044
to
1051
| let nonchart = | ||
| Chart.Point(nonex,res.NonSigBioitem |> Array.map (fun x -> x.Statistics)) | ||
| |> Chart.withLineStyle(Color=Color.fromKeyword Gray) | ||
| |> Chart.withTraceInfo("no change",Visible = Visible.True) | ||
|
|
||
| // negative significant changes | ||
| let negex = expected.[0 .. res.NegSigBioitem.Length-1] |
There was a problem hiding this comment.
let nonex = expected.[res.NegSigBioitem.Length-1 ..
let negex = expected.[0 .. res.NegSigBioitem.Length-1]Here the (res.NegSigBioitem.Length-1)th element is assigned to both, nonex and negex. I think an index error occurred.
There was a problem hiding this comment.
I think it should be:
let posExpected = expected.[res.NegSigBioitem.Length + res.NonSigBioitem.Length .. res.NegSigBioitem.Length + res.NonSigBioitem.Length + res.PosSigBioitem.Length-1]
let nonex = expected.[res.NegSigBioitem.Length .. res.NegSigBioitem.Length + res.NonSigBioitem.Length-1]
let negex = expected.[0 .. res.NegSigBioitem.Length-1]Please doublecheck
bvenn
reviewed
Dec 8, 2022
src/FSharp.Stats/Testing/SAM.fs
Outdated
Comment on lines
594
to
596
| let PosSigBioitem = getQvals |> Array.filter (fun x -> x.Statistics > upperCut) | ||
| let NegSigBioitem = getQvals |> Array.filter (fun x -> x.Statistics < lowerCut) | ||
| let NonSigBioitem = getQvals |> Array.filter (fun x -> x.Statistics >= lowerCut && x.Statistics <= upperCut) |
There was a problem hiding this comment.
shouldnt it be:
let PosSigBioitem = getQvals |> Array.filter (fun x -> x.Statistics >= upperCut)
let NegSigBioitem = getQvals |> Array.filter (fun x -> x.Statistics <= lowerCut)
let NonSigBioitem = getQvals |> Array.filter (fun x -> x.Statistics > lowerCut && x.Statistics < upperCut)Fix requested changes
Codecov Report
@@ Coverage Diff @@
## developer #237 +/- ##
=============================================
+ Coverage 43.36% 44.82% +1.46%
=============================================
Files 142 143 +1
Lines 14028 14302 +274
Branches 1892 1908 +16
=============================================
+ Hits 6083 6411 +328
+ Misses 7444 7365 -79
- Partials 501 526 +25
Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. |
bvenn
approved these changes
Jan 25, 2023
This was referenced Jan 31, 2023
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Please reference the issue(s) this PR is related to
Implementing SAM as in FR #236
Please list the changes introduced in this PR