Hello, I am working on R using the compareCluster package.
I have a gene list like this (with ENTREZID on top and logFC at the bottom):
head(genelist)
949101 945316 945807 947239 946699 945783 945780 94603
4.311420437 3.762809441 3.529820947 3.333709954 3.317216812 3.255953865 3.160993457 3.160993457
With say 1000 rows.
I want to extract a select specific list of ENREZID along with their logFC, such as for example:
948683
947293
947227
947693
948129
947872
944778
947968
944799
945102
944803
944982
944823
947969
948249
945238
947011
947673
946662
946625
948900
945328
947352
What codes do I use to make that execution on R?
1 answer
The genelist object you show looks more like a named vector (you can check with class(genelist)). If this is the case, you can extract the list by, for example:
genenames <- as.character(c(948683,947293,947227)) # set as character to avoid asking for positions instead of names
genelist_filtered <- genelist[genenames]
If I may ask, a follow up question, how about if my gene list looks like this, how can I extract the desired list of genes from this kind of dataframe:
head(genelist)
ENTREZID FC
1 947315 1.576377015
2 944895 -0.023717866
3 947758 -0.125816872
4 947761 0.104652669
5 946796 -0.045722731
6 948517 -0.028024538
These questions are generic R issues which may better fit in other forums such as Stack Overlow (and most probably have already been answered there or referred to basic R use courses). Nonetheless:
That last object is two-dimensional and may be filtered in different ways, one of which could be:
genenames <- as.character(c(948683,947293,947227))
genelist_filtered <- genelist[genelist$ENTREZID %in% genenames,]
Log in to answer this question.