Comments (4)
Yes, it is very easy. First read each patient data like this:
P1 <- load10x("filtered_gene_bc_matrices/hg19/")
P2 <- load10x("filtered_gene_bc_matrices/hg19/")
P3 <- load10x("filtered_gene_bc_matrices/hg19/")
...
P50 <- load10x("filtered_gene_bc_matrices/hg19/")
Then use the data.aggregation
function to make them into one file while also labeling each patient/condition.
Example for 3 patients:
my.data <- data.aggregation(samples = c("P1", "p2","P3"), condition.names = c("P1", "p2","P3"))
Then make an object:
my.obj <- make.obj(my.data)
my.obj
CPCA is for batch alignment, which you run instead of PCA step if you wish to do batch alignment.
from icellr.
Thank you for the quick reply. The CPCA can work for the batch effect,right? If it is, how can I use it to my data . Like the "my.obj <- iba(my.obj,dims = 1:30, k = 10,ba.method = "CPCA", method = "gene.model", gene.list = [email protected])" change the gene.model to orig.ident (sorry , I use the seurat)? OR if not, how can I integrate the data to aviod the batch effect.
from icellr.
Yes, you can replace [email protected]
with orig.ident
or any gene list. It is technically just a number of genes you want to use for this. It could be a list of top dispersed genes or top 1000-2000 expressed genes or combination of both or a set of genes you are interested in (eg. c(gene1,gene2,...)
).
from icellr.
Thank you very much!
from icellr.
Related Issues (20)
- Error: cannot allocate vector of size 6288.3 Gb HOT 1
- convert seurat object to iCellR object HOT 3
- Ploting colonotypes HOT 4
- converting old iCellR object to new object HOT 1
- TPM instead of count data & no conditions HOT 2
- Labelling cells with cluster HOT 4
- conds.to.plot in gene.plot not functional
- VDJ analysis: can I use filtered.contig? Error when I run clono.plot HOT 3
- Transform my seurat object into iCellR HOT 5
- Method for gene-gene correlations HOT 2
- How to normalize data with single condition? HOT 1
- 'replacement has 1 row, data has 0' when creating iCellR object HOT 3
- Transform my iCellR object into seurat? HOT 1
- no plots available for ADT data when using ADT + HTO
- Seeking help to create different types of plots HOT 3
- gg.cor produces incorrect plots
- can not using the iCellR ni rstudio when the plot setting the interactive =T
- data.scale question HOT 2
- an error message - running the run.knetl HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from icellr.