Commit f6809a82 authored by mariefbourdon's avatar mariefbourdon
Browse files

change version

parent 2054450f
"0","genos <- genos %>% filter(!Sample.ID %in% c(""StrainsA_1"", ""StrainsA_2"", ""StrainsB_1"",""StrainsB_2""))"
"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","
"
"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","
"
"1"," 3rd Qu.: 34.00 "
"1"," 3rd Qu.: 5.00 "
"1"," 3rd Qu.: 5.00 "
"1","
"
"1"," Max. :175.00 "
"1"," Max. :176.00 "
"1"," Max. :176.00 "
"1","
"
"0","tab2 <- mark_match(stuart_tab,ref=strains)"
"0",""
"0",""
"0","tab2 %>% filter(exclude_match==1)"
{"classes":["tbl_df","tbl","data.frame"],"ncol":8,"nrow":0}
\ No newline at end of file
{"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
{"chunk_definitions":[{"chunk_id":"culdjhv7njxmo","chunk_label":"unnamed-chunk-1","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","include":false,"label":"unnamed-chunk-1"},"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}],"doc_write_time":1623691782}
\ No newline at end of file
"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"
"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)"
"0","annot_mini <- read.csv(url(""https://raw.githubusercontent.com/kbroman/MUGAarrays/master/UWisc/mini_uwisc_v2.csv""))"
"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)"
{"classes":["data.frame"],"ncol":14,"nrow":6}
\ No newline at end of file
Package: stuart
Title: stuart
Version: 0.1.0
Version: 1.0.0
Authors@R:
person(given = "Marie",
family = "Bourdon",
......
......@@ -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)
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment