Issue for minimum p value #180
Comments
|
why does it convert to an error? The warning is there because is it
rarely sensible to attempt colocalisation if you do not have a confident
genetic signal, but it is a warning, and not an error.
On 29/11/2024 16:35, Lida Wang wrote:
Hi there,
I was wondering why coloc.abf doesn't work well for me if the min
pvalue is not small enough. Here is what I got;
The warning will turn into error and then it couldn't run properly.
out1 <- coloc.abf(dataset1,dataset2)
Error in check_dataset(d = dataset1, 1) : (converted from warning)
minimum p value is: 2.1471e-05 If this is what you expected, this is
not a problem. If this is not as small as you expected, please check
you supplied var(beta) and not sd(beta) for the varbeta argument. If
that's not the explanation, please check the 02_data vignette.
It is the same for check_dataset() function
check_dataset(d = dataset1, 1)
Error in check_dataset(d = dataset1, 1) :
(converted from warning) minimum p value is: 2.1471e-05
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check you supplied
var(beta) and not sd(beta) for the varbeta argument. If that's not
the explanation, please check the 02_data vignette.
But when I add warn.minp, it works well, while coloc.abf still return
error
check_dataset(d = dataset1, 1,warn.minp=1e-4)
NULL
—
Reply to this email directly, view it on GitHub
<#180>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAQWR2AH6BJWAMFKXMGWDCD2DCJWJAVCNFSM6AAAAABSXN2SFCVHI2DSMVQWIX3LMV43ASLTON2WKOZSG4YDKNJZGY4DAMA>.
You are receiving this because you are subscribed to this
thread.Message ID: ***@***.***>
--------------Y02t95Y0Tc05sPRu2r4WLpQy
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: 8bit
<!DOCTYPE html><html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
<p>why does it convert to an error? The warning is there because is
it rarely sensible to attempt colocalisation if you do not have a
confident genetic signal, but it is a warning, and not an error.<br>
</p>
<div class="moz-cite-prefix">On 29/11/2024 16:35, Lida Wang wrote:<br>
</div>
<blockquote type="cite" ***@***.***">
<p dir="auto">Hi there,</p>
<p dir="auto">I was wondering why coloc.abf doesn't work well for
me if the min pvalue is not small enough. Here is what I got;</p>
<p dir="auto">The warning will turn into error and then it
couldn't run properly.</p>
<p dir="auto">out1 <- coloc.abf(dataset1,dataset2)<br>
Error in check_dataset(d = dataset1, 1) : (converted from
warning) minimum p value is: 2.1471e-05 If this is what you
expected, this is not a problem. If this is not as small as you
expected, please check you supplied var(beta) and not sd(beta)
for the varbeta argument. If that's not the explanation, please
check the 02_data vignette.</p>
<p dir="auto">It is the same for check_dataset() function</p>
<blockquote>
<p dir="auto">check_dataset(d = dataset1, 1)<br>
Error in check_dataset(d = dataset1, 1) :<br>
(converted from warning) minimum p value is: 2.1471e-05<br>
If this is what you expected, this is not a problem.<br>
If this is not as small as you expected, please check you
supplied var(beta) and not sd(beta) for the varbeta argument.
If that's not the explanation, please check the 02_data
vignette.</p>
</blockquote>
<p dir="auto">But when I add warn.minp, it works well, while
coloc.abf still return error</p>
<blockquote>
<p dir="auto">check_dataset(d = dataset1, 1,warn.minp=1e-4)<br>
NULL</p>
</blockquote>
<p style="font-size:small;-webkit-text-size-adjust:none;color:#666;">—<br>
Reply to this email directly, <a href="#180" originalsrc="#180" shash="qFkpby2R4IsGkXyGp23r4V7BuUCyKi7tcPNas2RSXZ+ilkomqbRb6XCzbNDUDjXoRI4mLXl5qERZH+19eQANPS//gS68NJVHrOtOZ1rWPTvkrsoEr8nsvTP2p7AfCUBvZBgL0XLnN9Le4l3/N0/0Q5kTIRMEZKP1Sc3oTMcn1Cc=" moz-do-not-send="true">view it on GitHub</a>, or <a href="https://github.com/notifications/unsubscribe-auth/AAQWR2AH6BJWAMFKXMGWDCD2DCJWJAVCNFSM6AAAAABSXN2SFCVHI2DSMVQWIX3LMV43ASLTON2WKOZSG4YDKNJZGY4DAMA" originalsrc="https://github.com/notifications/unsubscribe-auth/AAQWR2AH6BJWAMFKXMGWDCD2DCJWJAVCNFSM6AAAAABSXN2SFCVHI2DSMVQWIX3LMV43ASLTON2WKOZSG4YDKNJZGY4DAMA" shash="X7C3d1BAYymTCAj7zwGY9weC2yKlR3mp7eJWsmvPGsNE6Z1nAdgepMfKhNDJZ8PNUD7GMUYpRWFIXSRpo7llYwGL3sfoLzI5AV3hLtqJdot0rZkwQag9zNTF4jm3TgQzvfrJpcA/xYvvCAKkZY465CovSr3hp3p71MldcBxnOp8=" moz-do-not-send="true">unsubscribe</a>.<br>
You are receiving this because you are subscribed to this
thread.<img src="https://github.com/notifications/beacon/AAQWR2HYHDNCT76QLSW3UA32DCJWJA5CNFSM6AAAAABSXN2SFCWGG33NNVSW45C7OR4XAZNFJFZXG5LFVJRW63LNMVXHIX3JMTHKCRBBQA.gif" alt="" moz-do-not-send="true" width="1" height="1"><span style="color: transparent; font-size: 0; display: none; visibility: hidden; overflow: hidden; opacity: 0; width: 0; height: 0; max-width: 0; max-height: 0; mso-hide: all">Message
ID: <span><chr1swallace/coloc/issues/180</span><span>@</span><span>github</span><span>.</span><span>com></span></span></p>
<script type="application/ld+json">[
{
***@***.***": "http://schema.org",
***@***.***": "EmailMessage",
"potentialAction": {
***@***.***": "ViewAction",
"target": "#180",
"url": "#180",
"name": "View Issue"
},
"description": "View this Issue on GitHub",
"publisher": {
***@***.***": "Organization",
"name": "GitHub",
"url": "https://github.com"
}
}
]</script>
</blockquote>
</body>
</html>
…--------------Y02t95Y0Tc05sPRu2r4WLpQy--
|
|
It shows error on my end and I could not figure why. Best, Lida |
|
Set options(warnings=1) and that should fix it
Sent from Outlook for Android<https://aka.ms/AAb9ysg>
…________________________________
From: Lida Wang ***@***.***>
Sent: Sunday, December 1, 2024 2:54:31 AM
To: chr1swallace/coloc ***@***.***>
Cc: Chris Wallace ***@***.***>; Comment ***@***.***>
Subject: Re: [chr1swallace/coloc] Issue for minimum p value (Issue #180)
It shows error on my end and I could not figure why.
Best, Lida
—
Reply to this email directly, view it on GitHub<#180 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAQWR2HW2342FDMTWCQ6O3D2DJ26PAVCNFSM6AAAAABSXN2SFCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMBZGUZTSMBYHA>.
You are receiving this because you commented.Message ID: ***@***.***>
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Hi there,
I was wondering why coloc.abf doesn't work well for me if the min pvalue is not small enough. Here is what I got;
The warning will turn into error and then it couldn't run properly.
It is the same for check_dataset() function
But when I add warn.minp, it works well
while coloc.abf still return error
The text was updated successfully, but these errors were encountered: