Merge two data sets
0
0
Entering edit mode
7.4 years ago
saj98 ▴ 140

Hello everyone

I have two RNA seq experiments, one done on tissue and the second one done on cells. I am looking to do cross correlation between the two experiments. I have CSV file for each experiment. I am interested to merge the two files in one CSV file. How I can merge the two files with matching the gene IDs? I am looking to do this step because I am interested to calculated the correlation of gene expression between invitro and invivo.

Thanks for help

RNA-Seq R • 2.9k views
ADD COMMENT
1
Entering edit mode

You can read CSV files into R separately, and use the gene IDs as rownames of data frame, then you can use cbind to merge two data frame.

ADD REPLY
1
Entering edit mode

R also has a merge function that is useful, and you can merge by gene ID.

ADD REPLY
0
Entering edit mode

Hello I used merge command, but I got this error message, any help or suggestion

> CP1.df <- read.csv(file.choose(), header = TRUE, sep = ",")
> CP2.df <- read.csv(file.choose(), header = TRUE, sep = ",")
> X=merge(CP1.df,CP2.df)
Error: cannot allocate vector of size 4.9 Gb
In addition: Warning messages:
1: In expand.grid(seq_len(nx), seq_len(ny)) :
  Reached total allocation of 20388Mb: see help(memory.size)
2: In expand.grid(seq_len(nx), seq_len(ny)) :
  Reached total allocation of 20388Mb: see help(memory.size)
3: In expand.grid(seq_len(nx), seq_len(ny)) :
  Reached total allocation of 20388Mb: see help(memory.size)
4: In expand.grid(seq_len(nx), seq_len(ny)) :
  Reached total allocation of 20388Mb: see help(memory.size)
>
ADD REPLY
0
Entering edit mode

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLY
0
Entering edit mode

did you try passing in a by argument to merge

ADD REPLY
0
Entering edit mode

check join in bash

ADD REPLY
0
Entering edit mode

Hello I got the figured out how to solve it, and I am sharing it with you

exporttab <- merge(x=dwd_nogap, y=dwd_gap, by.x='x1', by.y='x2', fill=-9999), and it was very useful.

ADD REPLY
0
Entering edit mode

Do you see why it initially failed, expanding to > 20Gb, though?

ADD REPLY

Login before adding your answer.

Traffic: 1461 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6