Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

liang2020: improve the annotation of the proteins from blank samples #19

Open
cvanderaa opened this issue Oct 5, 2021 · 0 comments
Open
Assignees

Comments

@cvanderaa
Copy link
Member

cvanderaa commented Oct 5, 2021

Improve this section:

# Assess the nature of the proteins
**Sections below are work in progress**
```{r, echo = FALSE}
knitr::opts_chunk$set(eval = FALSE)
```
Up to now, we saw that single-cells and
```{r}
universe <- rbindRowData(autoPOTS, i = grep("HeLa", names(autoPOTS)))
universe <- unique(universe$Leading.razor.protein)
```
## In many cells samples
### Biological process
```{r, fig.width=10}
common500 <- rbindRowData(autoPOTS, i = grep("500", names(autoPOTS)))
common500 <- unique(common500$Leading.razor.protein)
go_500 <- enrichGO(gene = common500,
OrgDb = org.Hs.eg.db,
keyType = "UNIPROT",
ont = "BP",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe = keys(org.Hs.eg.db, "UNIPROT"),
qvalueCutoff = 0.05,
minGSSize = 50,
maxGSSize = 200,
readable = FALSE,
pool = FALSE)
dotplot(go_500, showCategory = Inf)
```
### Cellular compartment
```{r, fig.height=10, fig.width = 8, message=FALSE}
go_blank_CC <- enrichGO(gene = common500,
OrgDb = org.Hs.eg.db,
keyType = "UNIPROT",
ont = "CC",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
# universe = keys(org.Hs.eg.db, "UNIPROT"),
universe = universe,
qvalueCutoff = 0.05,
minGSSize = 200,
maxGSSize = 1000,
readable = FALSE,
pool = FALSE)
dotplot(go_blank_CC, showCategory = Inf)
```
## In blanks
This indicates contamination by skin cells? Let
### Biological process
```{r, fig.height = 25, fig.width = 10}
common0 <- rbindRowData(autoPOTS, i = grep("_0cell", names(autoPOTS)))
common0 <- unique(common0$Leading.razor.protein)
go_blank <- enrichGO(gene = common0,
OrgDb = org.Hs.eg.db,
keyType = "UNIPROT",
ont = "BP",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe = keys(org.Hs.eg.db, "UNIPROT"),
qvalueCutoff = 0.05,
minGSSize = 50,
maxGSSize = 200,
readable = FALSE,
pool = FALSE)
dotplot(go_blank, showCategory = Inf)
```
### Cellular component
```{r, fig.height=10, fig.width = 8, message=FALSE}
go_blank_CC <- enrichGO(gene = common0,
OrgDb = org.Hs.eg.db,
keyType = "UNIPROT",
ont = "CC",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
# universe = keys(org.Hs.eg.db, "UNIPROT"),
universe = universe,
qvalueCutoff = 0.05,
minGSSize = 200,
maxGSSize = 1000,
readable = FALSE,
pool = FALSE)
dotplot(go_blank_CC, showCategory = Inf)
```
## In single-cells
```{r, fig.width=10}
commonSC <- rbindRowData(autoPOTS, i = grep("_1cell", names(autoPOTS)))
commonSC <- unique(commonSC$Leading.razor.protein)
go_sc <- enrichGO(gene = commonSC,
OrgDb = org.Hs.eg.db,
keyType = "UNIPROT",
ont = "BP",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe = universe,
qvalueCutoff = 0.05,
minGSSize = 50,
maxGSSize = 200,
readable = FALSE,
pool = FALSE)
dotplot(go_sc, showCategory = 20)
```

Based on the results, improve the sentence in the conclusion:

TODO add paragraph: single-cell signal ~ blank signal -> list
arguments => is autoPOTS really working for sc samples?

@cvanderaa cvanderaa self-assigned this Oct 5, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant