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Commit f6809a82 authored by mariefbourdon's avatar mariefbourdon
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.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/ccbr8kr5rmfiz/000002.csv deleted 100644 → 0
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"0","genos <- genos %>% filter(!Sample.ID %in% c(""StrainsA_1"", ""StrainsA_2"", ""StrainsB_1"",""StrainsB_2""))"
.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/ceekbogybpgbx/000002.csv deleted 100644 → 0
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"0","data(stuart_tab)"
"0","summary(stuart_tab)"
"1",""
"1"," marker "
"1"," allele_1 "
"1"," allele_2 "
"1"," n_HM1 "
"1","
"
"1"," Length:11125 "
"1"," Length:11125 "
"1"," Length:11125 "
"1"," Min. : 0.0 "
"1","
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"1"," Class :character "
"1"," Class :character "
"1"," Class :character "
"1"," 1st Qu.: 44.0 "
"1","
"
"1"," Mode :character "
"1"," Mode :character "
"1"," Mode :character "
"1"," Median :174.0 "
"1","
"
"1"," "
"1"," "
"1"," "
"1"," Mean :123.9 "
"1","
"
"1"," "
"1"," "
"1"," "
"1"," 3rd Qu.:176.0 "
"1","
"
"1"," "
"1"," "
"1"," "
"1"," Max. :176.0 "
"1","
"
"1",""
"1"," n_HM2 "
"1"," n_HT "
"1"," n_NA "
"1","
"
"1"," Min. : 0.00 "
"1"," Min. : 0.00 "
"1"," Min. : 0.00 "
"1","
"
"1"," 1st Qu.: 0.00 "
"1"," 1st Qu.: 0.00 "
"1"," 1st Qu.: 0.00 "
"1","
"
"1"," Median : 0.00 "
"1"," Median : 0.00 "
"1"," Median : 1.00 "
"1","
"
"1"," Mean : 19.92 "
"1"," Mean : 19.24 "
"1"," Mean : 12.91 "
"1","
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"1"," 3rd Qu.: 34.00 "
"1"," 3rd Qu.: 5.00 "
"1"," 3rd Qu.: 5.00 "
"1","
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"1"," Max. :175.00 "
"1"," Max. :176.00 "
"1"," Max. :176.00 "
"1","
"
.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/cgfik6q17v45t/000006.csv deleted 100644 → 0
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"0","tab2 <- mark_match(stuart_tab,ref=strains)"
"0",""
"0",""
"0","tab2 %>% filter(exclude_match==1)"
.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/cgfik6q17v45t/000007.metadata deleted 100644 → 0
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{"classes":["tbl_df","tbl","data.frame"],"ncol":8,"nrow":0}
\ No newline at end of file
.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/chunks.json
View file @ f6809a82
{"chunk_definitions":[{"chunk_id":"culdjhv7njxmo","chunk_label":"unnamed-chunk-1","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","include":false,"label":"unnamed-chunk-3"},"row":15,"row_count":1,"visible":true},{"chunk_id":"csetup_chunk","chunk_label":"setup","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","include":false,"label":"setup"},"row":31,"row_count":1,"visible":true},{"chunk_id":"cvrfzlkmsnd5m","chunk_label":"annot","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"annot"},"row":45,"row_count":1,"visible":true},{"chunk_id":"c0s26bf1pu5ys","chunk_label":"load","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"load"},"row":60,"row_count":1,"visible":true},{"chunk_id":"cxuyx1brxodqv","chunk_label":"strains","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"strains"},"row":73,"row_count":1,"visible":true},{"chunk_id":"ccbr8kr5rmfiz","chunk_label":"no_parent","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"no_parent"},"row":78,"row_count":1,"visible":true},{"chunk_id":"ceekbogybpgbx","chunk_label":"tab_mark","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"tab_mark"},"row":91,"row_count":1,"visible":true},{"chunk_id":"cgfik6q17v45t","chunk_label":"mark_match","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"mark_match"},"row":100,"row_count":1,"visible":true},{"chunk_id":"c4gkr1xb8o1a9","chunk_label":"mark_poly ex","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"mark_poly ex"},"row":109,"row_count":1,"visible":true},{"chunk_id":"cp87d27x07m61","chunk_label":"mark_prop ex","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"mark_prop ex"},"row":116,"row_count":1,"visible":true}],"default_chunk_options":{},"doc_write_time":1623085296,"working_dir":null}
\ No newline at end of file
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.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/cp87d27x07m61/000022.csv deleted 100644 → 0
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"0","tab2 <- mark_prop(tab2,cross=""F2"",pval=0.05)
"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
"2","Chi-squared approximation may be incorrect"
.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/csetup_chunk/000002.csv
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"0","library(dplyr)"
"2","
Attachement du package : ‘dplyr’
"
"2","The following objects are masked from ‘package:stats’:
filter, lag
"
"2","The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
"
"0","library(stuart)"
.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/cvrfzlkmsnd5m/000002.csv deleted 100644 → 0
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"0","annot_mini <- read.csv(url(""https://raw.githubusercontent.com/kbroman/MUGAarrays/master/UWisc/mini_uwisc_v2.csv""))"
.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/cxuyx1brxodqv/000006.csv deleted 100644 → 0
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"0","strains <- geno_strains(ref=annot_mini,geno=genos,par1=c(""StrainsA_1"",""StrainsA_2""),par2=c(""StrainsB_1"",""StrainsB_2""),name1=""parent1"",name2=""parent2"")"
"0","head(strains)"
.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/cxuyx1brxodqv/000007.metadata deleted 100644 → 0
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{"classes":["data.frame"],"ncol":14,"nrow":6}
\ No newline at end of file
DESCRIPTION
View file @ f6809a82
Package: stuart
Title: stuart
Version: 0.1.0
Version: 1.0.0
Authors@R:
person(given = "Marie",
family = "Bourdon",
......
vignettes/stuaRt.Rmd
View file @ f6809a82
......@@ -109,7 +109,7 @@ tab2 <- mark_poly(tab2)
head(tab2)
```
The `mark_prop()` function can be used to filter markers depending on the proportion of each genotype. Here, we have a F2 so we can use the "homo" argument in order to filter depending on the proportion of both homozygous genotype. If we have a N2, we can filter with the proportion of homozygous individuals with the "homo" argument and of heterozygous individuals with the hetero" argument. Moreover, this function allows to filter marker depending on the proportion on non genotyped animals. By defaults, markers for which more than 50% of individuals were not genotyped.
The `mark_prop()` function can be used to filter markers depending on the proportion of each genotype. Here, we have a F2 so we can use the "homo" argument in order to filter depending on the proportion of both homozygous genotype. If we have a N2, we can filter with the proportion of homozygous individuals with the "homo" argument and of heterozygous individuals with the "hetero" argument. Moreover, this function allows to filter marker depending on the proportion on non genotyped animals. By defaults, markers for which more than 50% of individuals were not genotyped.
```{r mark_prop ex}
tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
......
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