reactomePA error input file

# A tibble: 6 x 2 Entrezgene_ID log2fc <chr> <dbl> 1 14 -1.02 2 80755 -1.45 3 60496 -1.17 4 6059 -1.48 5 10061 -1.35 6 10006 -1.51

#load packages library(org.Hs.eg.db) library(DOSE) library(ReactomePA) ## feature 1: numeric vector geneList <- d[,2] ## feature 2: named vector names(geneList) <- as.character(d[,1]) ## feature 3: decreasing order geneList<- sort(geneList, decreasing = TRUE) head(geneList)

9 months ago by

russhh ♦ 5.5k

UK, U. Glasgow

russhh ♦ 5.5k wrote:

unlike when you subset a data-frame, when you subset a tibble using tbl[, col] syntax, you always receive a tibble. For a data.frame, extracting a single column in this way would return a vector. What you've done is extract geneList as a Nx1 tibble, and tried to set the names on that.

To extract a vector from a tibble, use genes <- tbl[[col]] syntax, and then use names(genes) <- tbl[[other_col]]

ADD COMMENT • link written 9 months ago by russhh ♦ 5.5k

Plus, if you already have tibble loaded, you can use it's deframe function to do this in one step: https://stackoverflow.com/a/56479548/1845650 ; genes <- tibble::deframe(d) . That only works for two-column data-frames: the first column becomes the vector-names and the second column becomes the vector-contents

ADD REPLY • link written 9 months ago by russhh ♦ 5.5k

There are several other ways of doing this mentioned in that SO thread, dplyr::pull for example

ADD REPLY • link written 9 months ago by russhh ♦ 5.5k

so if I use

genes <- tibble::deframe(d)

I should obtain already a vector with my values and their associated "names"?

ADD REPLY • link written 9 months ago by camillab. • 40

Hi! Thank you! so the code should be:

#load packages
library(org.Hs.eg.db)
library(DOSE)
library(ReactomePA)

## feature 1: numeric vector
genes <- d[[,2]]

## feature 2: named vector
names(genes) <- d[[,1]]

## feature 3: decreasing order
geneLIST <- sort(geneList, decreasing = TRUE)
head(geneList)

x <- enrichPathway(gene=geneLIST,pvalueCutoff=0.05, readable=T)

because it gives me this error when I use [[ ]] :

Error: Subscript can't be missing for tibbles in [[.

and if I do :

## feature 1: numeric vector
genes <- d[,2]

## feature 2: named vector
names(genes) <- d[,1]

I have the same results (and error) that before.

ADD REPLY • link modified 9 months ago • written 9 months ago by camillab. • 40

No, the code should be genes <- d[[2]]; names(genes) <- d[[1]]

ADD REPLY • link written 9 months ago by russhh ♦ 5.5k

On a tibble or data.frame, the [[ function extracts a column as a vector: `[[`(my_df, column_index). It takes the data.frame and a column index as argument; so when it's used as an operator it should look like my_df[[column_index]] (not my_df[[, column_index]])

ADD REPLY • link modified 9 months ago • written 9 months ago by russhh ♦ 5.5k

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