Comments (5)
kbroman
commented on September 14, 2024
R/qtl is intended for QTL analysis of data from simple crosses between inbred lines, such as a backcross or intercross. The input format is rather specific; see Chapter 2 of the R/qtl book.
The Data.csv file within the Data.zip file that you provide is tab-delimited, so you would need to use sep="\t" in the call to read.cross(), but the main problems are that you shouldn't include the founder strains, you would need many more than two individuals, and you would need to restructure the data file a bit; see the sample CSV data files at http://www.rqtl.org/sampledata/.
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DivijaGaniga
commented on September 14, 2024
Thank You. There are many more than two individuals in the analysis I just
sent part of the file . To re-structure the file Phenotype should be put on
columns which imay be difficult task as there are many number of rows for
particular phenotype.
…On Mon, Oct 29, 2018 at 1:35 PM Karl Broman ***@***.***> wrote:
R/qtl is intended for QTL analysis of data from simple crosses between
inbred lines, such as a backcross or intercross. The input format is rather
specific; see Chapter 2 of the R/qtl book <http://rqtl.org/book>.
The Data.csv file within the Data.zip file that you provide is
tab-delimited, so you would need to use sep="\t" in the call to
read.cross(), but the main problems are that you shouldn't include the
founder strains, you would need many more than two individuals, and you
would need to restructure the data file a bit; see the sample CSV data
files at http://www.rqtl.org/sampledata/.
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kbroman
commented on September 14, 2024
I don't completely understand what you mean, but you could could use the "csvr" format where the rows are phenotypes and then markers, and the columns are individuals. Here's an example from the R/qtl book, chapter 2 pg 29:
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DivijaGaniga
commented on September 14, 2024
I have two files for the same analysis one is my data and other is data
from other source for the same phenotype and I need to compare my data with
their data. So can I use "merge" function between the two files to compare
in R/qtl?
…On Tue, Oct 30, 2018 at 10:52 AM Karl Broman ***@***.***> wrote:
I don't completely understand what you mean, but you could could use the
"csvr" format where the rows are phenotypes and then markers, and the
columns are individuals. Here's an example from the R/qtl book
<http://rqtl.org/book>, chapter 2 pg 29:
[image: figure_2-4]
<https://user-images.githubusercontent.com/53972/47726801-3671d600-dc29-11e8-9082-c494122ba860.png>
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kbroman
commented on September 14, 2024
There's a c.cross() function that can be used to combine two crosses. Or you could load the two datasets, analyze them separately, and compare the results.
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Related Issues (20)
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