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mgledi / DiffLogo

DiffLogo: Comparative visualisation of sequence motifs
http://difflogo.com
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stuck on the matrix format #28

Open dabitz opened 6 years ago

dabitz commented 6 years ago

Hi, I am trying to run DiffLogo with your test matrices, but I am not succeeding, most likely by çaking some stupid mistake... Can you help me:

diffLogoFromPwm(pwm1 = "H1-hESC.pwm", pwm2 = "HeLa-S3.pwm") [1] "pwm must be of class matrix or data.frame. Trying to convert" [1] "pwm must be of class matrix or data.frame. Trying to convert" Error in FUN(if (length(d.call) < 2L) newX[, 1] else array(newX[, 1L], : invalid 'type' (character) of argument diffLogoFromPwm(pwm1 = "H1-hESC", pwm2 = "HeLa-S3") [1] "pwm must be of class matrix or data.frame. Trying to convert" [1] "pwm must be of class matrix or data.frame. Trying to convert" Error in FUN(if (length(d.call) < 2L) newX[, 1] else array(newX[, 1L], : invalid 'type' (character) of argument diffLogoFromPwm(pwm1 = "extdata/pwm/H1-hESC.pwm", pwm2 = "extdata/pwm/HeLa-S3.pwm") [1] "pwm must be of class matrix or data.frame. Trying to convert" [1] "pwm must be of class matrix or data.frame. Trying to convert" Error in FUN(if (length(d.call) < 2L) newX[, 1] else array(newX[, 1L], : invalid 'type' (character) of argument Best, André

mgledi commented 6 years ago

Hey dabitz, you can not use simple strings. You have to pass PWM-like structures. Have a look at page 7 of https://bioconductor.org/packages/release/bioc/manuals/DiffLogo/man/DiffLogo.pdf.