R Dataset / Package gap / crohn

How To Create a Barplot

The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.
Category
Visual
Instructional

How To Create a Stacked Barplot

The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.
Category
Visual
Instructional

How To Create a Pie Chart

The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.
Category
Instructional
Visual

How To Compute the Mean

The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.
Category
Numerical
Instructional

How To Create a Plot

The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.
Category
Visual
Instructional

How to Compute the Median

The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.
Category
Instructional
Numerical

Boxplot

Submitted by pmagunia on April 22, 2018 - 3:07 PM
The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.

Correlation Coefficient

Submitted by pmagunia on April 22, 2018 - 3:08 PM
The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.

Cumulative Frequency Histogram

Submitted by pmagunia on April 22, 2018 - 3:09 PM
The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.

Dotplot

Submitted by pmagunia on April 22, 2018 - 3:10 PM
The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.

Hollow Histogram

Submitted by pmagunia on April 22, 2018 - 3:10 PM
The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.

Numerical Summaries

Submitted by pmagunia on April 22, 2018 - 2:51 PM
The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.

Pie Chart

Submitted by pmagunia on April 22, 2018 - 3:11 PM
The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.

Plot

Submitted by pmagunia on April 22, 2018 - 3:07 PM
The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.

Ratio

Submitted by pmagunia on December 18, 2021 - 4:28 PM

Regression

Submitted by pmagunia on April 22, 2018 - 3:12 PM

Stem and Leaf Plots

Submitted by pmagunia on April 22, 2018 - 3:12 PM
The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.

Visual Summaries

Submitted by pmagunia on April 22, 2018 - 3:13 PM
The Drupal File ID of the selected dataset. The user may load another using the search bar on the operation's page.
Submitted by pmagunia on March 9, 2018 - 1:06 PM
<iframe src="https://embed.picostat.com/r-dataset-package-gap-crohn.html" frameBorder="0" width="100%" height="307px" />
Attachment Size
dataset-21865.csv 167.4 KB
Dataset License
GNU General Public License v2.0
Documentation License
GNU General Public License v2.0
Documentation

On this Picostat.com statistics page, you will find information about the crohn data set which pertains to Crohn's disease data. The crohn data set is found in the gap R package. Try to load the crohn data set in R by issuing the following command at the console data("crohn"). This may load the data into a variable called crohn. If R says the crohn data set is not found, you can try installing the package by issuing this command install.packages("gap") and then attempt to reload the data with library("gap") followed by data("crohn"). Perhaps strangley, if R gives you no output after entering a command, it means the command succeeded. If it succeeded you can see the data by typing crohn at the command-line which should display the entire dataset.

If you need to download R, you can go to the R project website. You can download a CSV (comma separated values) version of the crohn R data set. The size of this file is about 171,419 bytes.


Crohn's disease data

Description

The data set consist of 103 common (>5% minor allele frequency) SNPs genotyped in 129 trios from an European-derived population. These SNPs are in a 500-kb region on human chromosome 5q31 implicated as containing a genetic risk factor for Crohn disease.

The positions, names and haplotype blocks reported are as follows, 

274044   IGR1118a_1	BLOCK 1
274541   IGR1119a_1	*
286593   IGR1143a_1	*
287261   IGR1144a_1	*
299755   IGR1169a_2	*
324341   IGR1218a_2	*
324379   IGR1219a_2	*
358048   IGR1286a_1	BLOCK 1
366811	 TSC0101718
395079   IGR1373a_1	BLOCK 2
396353   IGR1371a_1	*
397334   IGR1369a_2	*
397381   IGR1369a_1	*
398352   IGR1367a_1	BLOCK 2
411823   IGR2008a_2
411873   IGR2008a_1	BLOCK 3
412456   IGR2010a_3	*
413233   IGR2011b_1	*
415579   IGR2016a_1	*
417617   IGR2020a_15	*
419845   IGR2025a_2	*
424283   IGR2033a_1	*
425376   IGR2036a_2	*
425549   IGR2036a_1	BLOCK 3
433467   IGR2052a_1	BLOCK 4
435282   IGR2055a_1	*
437682   IGR2060a_1	*
438883   IGR2063b_1	*
443565   IGR2072a_2	*
443750   IGR2073a_1	*
445337   IGR2076a_1	*
447791   IGR2081a_1	*
449895   IGR2085a_2	*
455246   IGR2096a_1	*
463136   IGR2111a_3	BLOCK 4
482171   IGR2150a_1	BLOCK 5
485828   IGR2157a_1	*
495082   IGR2175a_2	*
506266   IGR2198a_1	*
506890   IGR2199a_1	BLOCK 5
507208   IGR2200a_1	BLOCK 6
508338   IGR2202a_1	*
508858   IGR2203a_1	*
510951   IGR2207a_1	*
518478   IGR2222a_2	BLOCK 6
519387   IGR2224a_2	BLOCK 7
519962   IGR2225a_1	*
520521   IGR2226a_3	*
522600   IGR2230a_1	*
525243   IGR2236a_1	*	
529556   IGR2244a_4	*
532363   IGR2250a_4	*
545062   IGR2276a_1	*
553189   IGR2292a_1	*
570978   IGR3005a_1	*
571022   IGR3005a_2	*
576586   IGR3016a_1	*
577141   IGR3018a_2	*
577838   IGR3019a_2	*
578122   IGR3020a_1	*
579217   IGR3022a_1	*
579529   IGR3023a_1	*
579818   IGR3023a_3	*
582651   IGR3029a_1	*
582948   IGR3029a_2	*
583131   IGR3030a_1	*
587836   IGR3039a_1	*
590425   IGR3044a_1	*
590585   IGR3045a_1	*
594115   IGR3051a_1	*
594812   IGR3053a_1	*
598805   IGR3061a_1	*
601294   IGR3066a_1	*
608759   IGR3081a_1	*
610447   IGR3084a_1	*
611177   IGR3086a_1	BLOCK 7
613488   IGR3090a_1
616241   IGR3096a_1	BLOCK 8
616763   IGR3097a_1	*
617299   IGR3098a_1	*
626881   IGR3117a_1	*
633786   IGR3131a_1	*
635072   IGR3134a_1	*
637441   IGR3138a_1	BLOCK 8
648564   IGR3161a_1
649061   IGR3162a_1	BLOCK 9
649903   IGR3163a_1	*
657234   IGR3178a_1	*
662077   IGR3188a_1	*
662819   IGR3189a_2	*
676688   IGRX100a_1	BLOCK 9
683387   IGR3230a_1	BLOCK 10
686249   IGR3236a_1	*
692320   IGR3248a_1	*
718291   IGR3300a_2	*
730313   IGR3324a_1	*
731025   IGR3326a_1	*
738461   IGR3340a_1	BLOCK 10
871978   GENS021ex1_2	BLOCK 11
877571   GENS020ex3_3	*
877671   GENS020ex3_2	*
877809   GENS020ex3_1	*
890710   GENS020ex1_1	BLOCK 11

However it has been updated after the paper was published (posted on http://www.broad.mit.edu/humgen/IBD5/haplodata.html)

An example use of the data is with the following paper, Kelly M. Burkett, Celia M. T. Greenwood, BradMcNeney, Jinko Graham. Gene genealogies for genetic association mapping, with application to Crohn's disease. Fron Genet 2013, 4(260) doi: 10.3389/fgene.2013.00260

Usage

data(crohn)

Format

A data frame containing 387 rows and 212 columns

Source

MJ Daly, JD Rioux, SF Schaffner, TJ Hudson, ES Lander (2001) High-resolution haplotype structure in the human genome Nature Genetics 29:229-232 

--

Dataset imported from https://www.r-project.org.
Picostat Manual
How To Register With a Username
  1. Go to the user registration page.
  2. Enter a username and email address into the form.
  3. Answer the ReCaptcha (this is used to prevent spam).
  4. Click Submit.
  5. Click the link that was sent to the email address you registered with.
  6. Clicking the link will open another page on Picostat where you can select a password.
  7. Click Save and enter any profile details you wish to enter.
How To Register With Google Single Sign On (SSO)
  1. Go to the user login page.
  2. Click the Google button that says "Sign in with Google". This will redirect you to a page controlled by Google.
  3. Enter your Google username and password if you are not already authenticated.
  4. Review the Picostat Terms of Use and Privacy Policy. Then submit the Google form if you accept the terms.
  5. Google will redirect you back to Picostat with your new account created and you will be logged in.
  6. Enter any profile details you wish to share.
How To Login With a Username and Password
  1. Go to the user login page.
  2. Enter your username and password that you registered with.
  3. Click "Login". You will be redirected to your user homepage authenticated.
How To Login With Google Single Sign On (SSO)
  1. Go to the user login page.
  2. Click the button that says "Sign in with Google".
  3. If you already registered with Picostat via Google SSO, you will be redirected to your user homepage authenticated.
How To Import a Dataset
  1. Create a Picostat account or login with your existing picostat account (see above).
  2. Go to the dataset import page.
  3. Select a license for the dataset. The default is "No License" but allows Picostat to host a copy of the dataset as per the privacy policy. You may wish to uncheck the "Public" option if you do not wish to share your dataset with others. R Datasets that come by downloading R have a GNU General Public License v3.0 which may also be selected from the Picostat dropdown.
  4. Enter a title for the dataset
  5. Choose a dataset input methods. Available options include:
    • Random data - this populates your dataset with random numbers between 0 and 100. You can specify the number of rows and columns for the random dataset.
    • CSV, TSV or TXT file - you will have the option upload a file within the current file size limit and also specify the header and whether or not the dataset is a contingency table. With contingency tables, the first column becomes a label for the rows. Currently with Picostat, there is limited support for contingency tables. Choose "Yes" to the Header option if the first line of the data contains titles for the rows. Also choose the Separator for the dataset. A separator is what breaks the data up. In some cases, a comma would separate data values in a row. You will also have the option to add documentation in the form keyboarded text and also uploaded documentation attachments. You can also specify a license for the documentation.
    • Copy and Paste. This selection contains many of the same fields as importing a file with an additional textarea to copy and paste data to.
    • Empty dataset. Start with a blank dataset and manually add data with the Picostat dataset editor.
    • Excel file - Choose this option if you would like to convert your Excel spreadsheet to a Picostat dataset. With this selection, you will have the option to specify whether to use the first row in the Excel file as column names. If you would like to choose a specific sheet to use, you can also specify with entering its name in the text input.
    • sas7bdat file - SAS is a powerful statistical software package that has its own proprietary file format. Choose this option if you are importing a SAS file.
    • SPSS sav file - SPSS is a statistical package owned by IBM. You can import SPSS files by choosing this option.
  6. Choose whether or not the dataset contains a header. Some of the dataset input methods allow you to specify whether or not a Header exists on the file. Sometimes dataset files contain a Header as the first row which names the columns. If you choose "Yes" to this, the first row in the dataset will become column headers.
  7. You can also add documentation and specify a documentation license. This can be used to help explain your dataset to those unfamiliar with it.
  8. Choose whether or not to upload an supporting attachments.
  9. Pass the captcha. To prevent spam submissions, Picostat has a captcha which is used to prevent automated submissions by bots.
  10. Choose a privacy setting for the dataset. You can also specify whether or not the dataset is Public. If you uncheck this setting, only you and the Picostat administrator will be able to view the dataset.
  11. Submit the form. Once the form is validated, you will be redirected to the dataset homepage where you can choose to edit or perform statistical operations on the dataset.
How To Perform Statistical Analysis with Picostat
  1. Go to any dataset homepage. You can get a full list at the dashboard.
  2. Near the top of the page there will be two drop downs. One for analysis and one for education. Here we will choose Analyis. Choose from one of the following:
    • Numerical Summaries - Here you can get the:
      1. Arithmetic mean
      2. Median
      3. Quartiles
      4. Minimum and Maximum
      5. Stem-and-leaf plot
      6. Standard deviation and Variance
      7. IQR
      8. Cumulative frequencies
    • Plot - a plot of two columns on the cartesian coordinate system
    • Boxplot - a Boxplot (box-and-whisker plot) of a column.
    • Correlation Coefficient - Compute the correlation coefficient between two columns.
    • Cumulative Frequency Histogram - Display a cumulative frequency histogram
    • Dotplot
    • Hollow Histogram - Plot two columns on the same histogram with a different color for each column.
    • Pie Chart
    • Regression - Perform a simple linear regression and compute the p-value and regression line. Also plots the data with the regression line.
    • Stem and Leaf Plots - Plot a one or two-sided stem-and-leaf plot from one or two columns respectively.
    • Visual Summaries - plots the following:
      1. Frequency Histogram
      2. Relative Frequency Histogram
      3. Cumulative Frequency Histogram
      4. Boxplot (Box-and-whisker plot)
      5. Dotplot
  3. PDF - Check this box if you want to download a PDF of the output from the statistical analysis application.
  4. HTML - Check this box if you want a link to the HTML page created with the application.
  5. R File - Check this box if you want a link to download the R commands used to generate output from this statistical application. You should be able to copy the commands verbatim into R Studio or R to recreate the analysis.
How To Use Educational Applications with Picostat
  1. Go to any dataset homepage. You can get a full list at the dashboard.
  2. Near the top of the page there will be two drop downs. One for analysis and one for education. Here we will choose Education. Choose from one of the following:
    • How To Create a Barplot - This will show you how to create a bar chart after selecting a column with the mouse.
    • How To Create a Stacked Barplot - This application will show you how to create a stacked bar plot from a column vector.
    • How To Create a Pie Chart - This application will show you how to create a pie chart from a column of data
    • How To Compute the Mean - This application will show you how to compute the mean from a column vector
    • How To Create a Plot - This app will show you how to plot two columns in the cartesian coordinate system.
    • How To Compute the Media - This statisistical app will show you how to compute the median from a column vector.
  3. PDF - Check this box if you want to download a PDF of the output from the education application.
  4. HTML - Check this box if you want a link to the HTML page created with the application.
Recent Queries For This Dataset

No queries made on this dataset yet.
Title Authored on Content type
R Dataset / Package wooldridge / driving March 9, 2018 - 1:06 PM Dataset
R Dataset / Package ISLR / College March 9, 2018 - 1:06 PM Dataset
R Dataset / Package Ecdat / Bwages March 9, 2018 - 1:06 PM Dataset
R Dataset / Package cluster / animals March 9, 2018 - 1:06 PM Dataset
R Dataset / Package Ecdat / Clothing March 9, 2018 - 1:06 PM Dataset
Title
Point estimation
Tutorial: How healthy is the Starbucks menu?
Tutorial: Which Animal Has the Highest Brain To Body Weight Ratio?
Picostat Manual
Title Link
Quiz: Brain To Body Weight Ratio

Requires login.
Quiz: Analysis of the Starbucks menu

Requires login.