How to pull logFC values for a select ENTREZID from a gene-list on R?

Question

[tpm]

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?

Answer 1

[Papyrus]

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]

[tpm]

Thank you very much.

[tpm]

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

[Papyrus]

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,]

[tpm]

Million thank you. I honestly did not know I could use StackOverflow. I am still a newbie on R :)). Thank you for the clarity.